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1. Genomics of adaptive evolution in the woolly mammoth

Author: Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pecnerova, Patricia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter, van der Valk, Tom, Dalén, Love, Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pecnerova, Patricia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter, van der Valk, Tom, and Dalén, Love
Abstract: Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of tradi-tional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
Published: 2023
Full Text: View/download PDF

2. Genomics of adaptive evolution in the woolly mammoth

Author: Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pečnerová, Patrícia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter D., van der Valk, Tom, Dalén, Love, Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pečnerová, Patrícia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter D., van der Valk, Tom, and Dalén, Love
Abstract: Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
Published: 2023

3. Genomics of adaptive evolution in the woolly mammoth

Author: Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pečnerová, Patrícia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter D., van der Valk, Tom, Dalén, Love, Díez-del-Molino, David, Dehasque, Marianne, Chacón-Duque, J. Camilo, Pečnerová, Patrícia, Tikhonov, Alexei, Protopopov, Albert, Plotnikov, Valeri, Kanellidou, Foteini, Nikolskiy, Pavel, Mortensen, Peter, Danilov, Gleb K., Vartanyan, Sergey, Gilbert, M. Thomas P., Lister, Adrian M., Heintzman, Peter D., van der Valk, Tom, and Dalén, Love
Abstract: Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
Published: 2023

4. Grey wolf genomic history reveals a dual ancestry of dogs.

Author: Bergström, Anders, Bergström, Anders, Stanton, David WG, Taron, Ulrike H, Frantz, Laurent, Sinding, Mikkel-Holger S, Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M, Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V, Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R, Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C, Swali, Pooja, Conard, Nicholas J, Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F, Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T, Ivanova, Varvara V, Janssens, Luc, Jennings, Richard P, Kasparov, Aleksei K, Kirillova, Irina V, Kurmaniyazov, Islam, Kuzmin, Yaroslav V, Kosintsev, Pavel A, Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O'Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y, Perri, Angela R, Pilot, Małgorzata, Pitulko, Vladimir V, Plotnikov, Valerii V, Protopopov, Albert V, Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F, Zazula, Grant, Crombé, Philippe, Hansen, Anders J, Willerslev, Eske, Leonard, Jennifer A, Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J, Hofreiter, Michael, Gilbert, M Thomas P, Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, Skoglund, Pontus, Bergström, Anders, Bergström, Anders, Stanton, David WG, Taron, Ulrike H, Frantz, Laurent, Sinding, Mikkel-Holger S, Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M, Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V, Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R, Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C, Swali, Pooja, Conard, Nicholas J, Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F, Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T, Ivanova, Varvara V, Janssens, Luc, Jennings, Richard P, Kasparov, Aleksei K, Kirillova, Irina V, Kurmaniyazov, Islam, Kuzmin, Yaroslav V, Kosintsev, Pavel A, Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O'Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y, Perri, Angela R, Pilot, Małgorzata, Pitulko, Vladimir V, Plotnikov, Valerii V, Protopopov, Albert V, Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F, Zazula, Grant, Crombé, Philippe, Hansen, Anders J, Willerslev, Eske, Leonard, Jennifer A, Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J, Hofreiter, Michael, Gilbert, M Thomas P, Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus
Abstract: The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Published: 2022

5. Grey wolf genomic history reveals a dual ancestry of dogs

Author: Bergström, Anders, Stanton, David W. G., Taron, Ulrike H., Frantz, Laurent, Sinding, Mikkel-Holger S., Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M., Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V., Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R., Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C., Swali, Pooja, Conard, Nicholas J., Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F., Drucker, Dorothée G., Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T., Ivanova, Varvara V., Janssens, Luc, Jennings, Richard P., Kasparov, Aleksei K., Kirillova, Irina V., Kurmaniyazov, Islam, Kuzmin, Yaroslav V., Kosintsev, Pavel A., Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O'Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y., Perri, Angela R., Pilot, Małgorzata, Pitulko, Vladimir V., Plotnikov, Valerii V., Protopopov, Albert V., Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F., Zazula, Grant, Crombé, Philippe, Hansen, Anders J., Willerslev, Eske, Leonard, Jennifer A., Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J., Hofreiter, Michael, Gilbert, M. Thomas P., Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, Skoglund, Pontus, Bergström, Anders, Stanton, David W. G., Taron, Ulrike H., Frantz, Laurent, Sinding, Mikkel-Holger S., Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M., Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V., Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R., Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C., Swali, Pooja, Conard, Nicholas J., Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F., Drucker, Dorothée G., Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T., Ivanova, Varvara V., Janssens, Luc, Jennings, Richard P., Kasparov, Aleksei K., Kirillova, Irina V., Kurmaniyazov, Islam, Kuzmin, Yaroslav V., Kosintsev, Pavel A., Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O'Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y., Perri, Angela R., Pilot, Małgorzata, Pitulko, Vladimir V., Plotnikov, Valerii V., Protopopov, Albert V., Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F., Zazula, Grant, Crombé, Philippe, Hansen, Anders J., Willerslev, Eske, Leonard, Jennifer A., Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J., Hofreiter, Michael, Gilbert, M. Thomas P., Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus
Abstract: The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Published: 2022
Full Text: View/download PDF

6. Grey wolf genomic history reveals a dual ancestry of dogs.

Author: Bergström, Anders, Bergström, Anders, Stanton, David WG, Taron, Ulrike H, Frantz, Laurent, Sinding, Mikkel-Holger S, Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M, Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V, Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R, Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C, Swali, Pooja, Conard, Nicholas J, Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F, Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T, Ivanova, Varvara V, Janssens, Luc, Jennings, Richard P, Kasparov, Aleksei K, Kirillova, Irina V, Kurmaniyazov, Islam, Kuzmin, Yaroslav V, Kosintsev, Pavel A, Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O'Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y, Perri, Angela R, Pilot, Małgorzata, Pitulko, Vladimir V, Plotnikov, Valerii V, Protopopov, Albert V, Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F, Zazula, Grant, Crombé, Philippe, Hansen, Anders J, Willerslev, Eske, Leonard, Jennifer A, Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J, Hofreiter, Michael, Gilbert, M Thomas P, Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, Skoglund, Pontus, Bergström, Anders, Bergström, Anders, Stanton, David WG, Taron, Ulrike H, Frantz, Laurent, Sinding, Mikkel-Holger S, Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M, Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V, Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R, Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C, Swali, Pooja, Conard, Nicholas J, Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F, Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T, Ivanova, Varvara V, Janssens, Luc, Jennings, Richard P, Kasparov, Aleksei K, Kirillova, Irina V, Kurmaniyazov, Islam, Kuzmin, Yaroslav V, Kosintsev, Pavel A, Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O'Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y, Perri, Angela R, Pilot, Małgorzata, Pitulko, Vladimir V, Plotnikov, Valerii V, Protopopov, Albert V, Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F, Zazula, Grant, Crombé, Philippe, Hansen, Anders J, Willerslev, Eske, Leonard, Jennifer A, Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J, Hofreiter, Michael, Gilbert, M Thomas P, Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus
Abstract: The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Published: 2022

7. Grey wolf genomic history reveals a dual ancestry of dogs

Author: Bergström, Anders, Stanton, David W. G., Taron, Ulrike H., Frantz, Laurent, Sinding, Mikkel Holger S., Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M., Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V., Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R., Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C., Swali, Pooja, Conard, Nicholas J., Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F., Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T., Ivanova, Varvara V., Janssens, Luc, Jennings, Richard P., Kasparov, Aleksei K., Kirillova, Irina V., Kurmaniyazov, Islam, Kuzmin, Yaroslav V., Kosintsev, Pavel A., Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O’Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y., Perri, Angela R., Pilot, Małgorzata, Pitulko, Vladimir V., Plotnikov, Valerii V., Protopopov, Albert V., Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F., Zazula, Grant, Crombé, Philippe, Hansen, Anders J., Willerslev, Eske, Leonard, Jennifer A., Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J., Hofreiter, Michael, Gilbert, M. Thomas P., Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, Skoglund, Pontus, Bergström, Anders, Stanton, David W. G., Taron, Ulrike H., Frantz, Laurent, Sinding, Mikkel Holger S., Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M., Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V., Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R., Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C., Swali, Pooja, Conard, Nicholas J., Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F., Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T., Ivanova, Varvara V., Janssens, Luc, Jennings, Richard P., Kasparov, Aleksei K., Kirillova, Irina V., Kurmaniyazov, Islam, Kuzmin, Yaroslav V., Kosintsev, Pavel A., Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O’Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y., Perri, Angela R., Pilot, Małgorzata, Pitulko, Vladimir V., Plotnikov, Valerii V., Protopopov, Albert V., Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F., Zazula, Grant, Crombé, Philippe, Hansen, Anders J., Willerslev, Eske, Leonard, Jennifer A., Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J., Hofreiter, Michael, Gilbert, M. Thomas P., Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus
Abstract: The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Published: 2022

8. Grey wolf genomic history reveals a dual ancestry of dogs

Author: Bergström, Anders, Stanton, David W. G., Taron, Ulrike H., Frantz, Laurent, Sinding, Mikkel Holger S., Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M., Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V., Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R., Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C., Swali, Pooja, Conard, Nicholas J., Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F., Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T., Ivanova, Varvara V., Janssens, Luc, Jennings, Richard P., Kasparov, Aleksei K., Kirillova, Irina V., Kurmaniyazov, Islam, Kuzmin, Yaroslav V., Kosintsev, Pavel A., Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O’Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y., Perri, Angela R., Pilot, Małgorzata, Pitulko, Vladimir V., Plotnikov, Valerii V., Protopopov, Albert V., Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F., Zazula, Grant, Crombé, Philippe, Hansen, Anders J., Willerslev, Eske, Leonard, Jennifer A., Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J., Hofreiter, Michael, Gilbert, M. Thomas P., Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, Skoglund, Pontus, Bergström, Anders, Stanton, David W. G., Taron, Ulrike H., Frantz, Laurent, Sinding, Mikkel Holger S., Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M., Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V., Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R., Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C., Swali, Pooja, Conard, Nicholas J., Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F., Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T., Ivanova, Varvara V., Janssens, Luc, Jennings, Richard P., Kasparov, Aleksei K., Kirillova, Irina V., Kurmaniyazov, Islam, Kuzmin, Yaroslav V., Kosintsev, Pavel A., Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O’Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y., Perri, Angela R., Pilot, Małgorzata, Pitulko, Vladimir V., Plotnikov, Valerii V., Protopopov, Albert V., Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F., Zazula, Grant, Crombé, Philippe, Hansen, Anders J., Willerslev, Eske, Leonard, Jennifer A., Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J., Hofreiter, Michael, Gilbert, M. Thomas P., Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus
Abstract: The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Published: 2022

9. The origins and spread of domestic horses from the Western Eurasian steppes.

Author: Librado, Pablo, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A, Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A, Kovalev, Alexey A, Alquraishi, Saleh, Alfarhan, Ahmed H, Al-Rasheid, Khaled AS, Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-Del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G, Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E, Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E, Anisimov, Mikhail A, Nikolskiy, Pavel A, Pavlova, Elena Y, Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N, Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A, Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Librado, Pablo, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A, Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A, Kovalev, Alexey A, Alquraishi, Saleh, Alfarhan, Ahmed H, Al-Rasheid, Khaled AS, Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-Del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G, Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E, Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E, Anisimov, Mikhail A, Nikolskiy, Pavel A, Pavlova, Elena Y, Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N, Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A, Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, and Zhumatayev, Rinat
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.
Published: 2021

10. Million-year-old DNA sheds light on the genomic history of mammoths.

Author: van der Valk, Tom, van der Valk, Tom, Pečnerová, Patrícia, Díez-Del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A, Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D, Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M, Götherström, Anders, Dalén, Love, van der Valk, Tom, van der Valk, Tom, Pečnerová, Patrícia, Díez-Del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A, Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D, Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M, Götherström, Anders, and Dalén, Love
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
Published: 2021

11. Million-year-old DNA sheds light on the genomic history of mammoths.

Author: van der Valk, Tom, van der Valk, Tom, Pečnerová, Patrícia, Díez-Del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A, Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D, Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M, Götherström, Anders, Dalén, Love, van der Valk, Tom, van der Valk, Tom, Pečnerová, Patrícia, Díez-Del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A, Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D, Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M, Götherström, Anders, and Dalén, Love
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
Published: 2021

12. The origins and spread of domestic horses from the Western Eurasian steppes.

Author: Librado, Pablo, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A, Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A, Kovalev, Alexey A, Alquraishi, Saleh, Alfarhan, Ahmed H, Al-Rasheid, Khaled AS, Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-Del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G, Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E, Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E, Anisimov, Mikhail A, Nikolskiy, Pavel A, Pavlova, Elena Y, Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N, Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A, Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Librado, Pablo, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A, Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A, Kovalev, Alexey A, Alquraishi, Saleh, Alfarhan, Ahmed H, Al-Rasheid, Khaled AS, Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-Del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G, Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E, Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E, Anisimov, Mikhail A, Nikolskiy, Pavel A, Pavlova, Elena Y, Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N, Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A, Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, and Zhumatayev, Rinat
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.
Published: 2021

13. Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

Author: Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya, Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, Lister, Adrian M., Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya, Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, and Lister, Adrian M.
Abstract: To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago.
Published: 2021
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14. Million-year-old DNA sheds light on the genomic history of mammoths

Author: van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, Dalén, Love, van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, and Dalén, Love
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back intothe Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale(1), the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago(2). Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
Published: 2021
Full Text: View/download PDF

15. Million-year-old DNA sheds light on the genomic history of mammoths

Author: van der Valk, Tom, Pecnerova, Patricia, Diez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Saglican, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, Dalén, Love, van der Valk, Tom, Pecnerova, Patricia, Diez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Saglican, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, and Dalén, Love
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution., These authors contributed equally: Tom van der Valk, Patrícia Pečnerová, David Díez-del-Molino
Published: 2021
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16. The origins and spread of domestic horses from the Western Eurasian steppes

Author: Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, Orlando, Ludovic, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, and Orlando, Ludovic
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12., Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12.
Published: 2021

17. Million-year-old DNA sheds light on the genomic history of mammoths

Author: van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, Dalén, Love, van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, and Dalén, Love
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
Published: 2021

18. The origins and spread of domestic horses from the Western Eurasian steppes

Author: Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, Orlando, Ludovic, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, and Orlando, Ludovic
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12., Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12.
Published: 2021

19. Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

Author: Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya I., Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, Lister, Adrian M., Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya I., Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, and Lister, Adrian M.
Abstract: To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago.
Published: 2021

20. Million-year-old DNA sheds light on the genomic history of mammoths

Author: van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, Dalén, Love, van der Valk, Tom, Pečnerová, Patrícia, Díez-del-Molino, David, Bergström, Anders, Oppenheimer, Jonas, Hartmann, Stefanie, Xenikoudakis, Georgios, Thomas, Jessica A., Dehasque, Marianne, Sağlıcan, Ekin, Fidan, Fatma Rabia, Barnes, Ian, Liu, Shanlin, Somel, Mehmet, Heintzman, Peter D., Nikolskiy, Pavel, Shapiro, Beth, Skoglund, Pontus, Hofreiter, Michael, Lister, Adrian M., Götherström, Anders, and Dalén, Love
Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780–560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
Published: 2021

21. The origins and spread of domestic horses from the Western Eurasian steppes

Author: Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan,Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean‐Marc, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lõugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Toleubaev, Abdesh, Gerber, Daniel, Kiss, Viktória, Anna Szécsényi-Nagy, Mende, Balazs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Morgunova, Nina L., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Kuznetsova, Tatyana V., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Lordkipanidze, David, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Marzullo, Matilde, Valenzuela-Lamas, Silvia, Albizuri, Silvia, Nieto-Espinet, Ariadna, Iborra Eres, María Pilar, Lira, Jaime, Rodríguez González, Esther, Celestino Pérez, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Prato, Ornella, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Gaunitz, Charleen, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Chauvey, Lorelei, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Seguin-Orlando, Andaine, Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Sarkissian, Clio Der, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Southon, John, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus, Kristiansen, Kristian, Shapiro, Beth, Wincker, Patrick, Outram, Alan K., Orlando, Ludovic, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A.S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Álvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan,Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean‐Marc, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lõugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Toleubaev, Abdesh, Gerber, Daniel, Kiss, Viktória, Anna Szécsényi-Nagy, Mende, Balazs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Morgunova, Nina L., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Kuznetsova, Tatyana V., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Lordkipanidze, David, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Marzullo, Matilde, Valenzuela-Lamas, Silvia, Albizuri, Silvia, Nieto-Espinet, Ariadna, Iborra Eres, María Pilar, Lira, Jaime, Rodríguez González, Esther, Celestino Pérez, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Prato, Ornella, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Gaunitz, Charleen, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Chauvey, Lorelei, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Seguin-Orlando, Andaine, Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Sarkissian, Clio Der, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Southon, John, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus, Kristiansen, Kristian, Shapiro, Beth, Wincker, Patrick, Outram, Alan K., Orlando, Ludovic, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A.S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Álvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, and Tunia, Krzysztof
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture.
Published: 2021

22. Combining Bayesian age models and genetics to investigate population dynamics and extinction of the last mammoths in northern Siberia

Author: Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya I., Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, Lister, Adrian M., Dehasque, Marianne, Pečnerová, Patrícia, Muller, Héloïse, Tikhonov, Alexei, Nikolskiy, Pavel, Tsigankova, Valeriya I., Danilov, Gleb K., Díez-del-Molino, David, Vartanyan, Sergey, Dalén, Love, and Lister, Adrian M.
Abstract: To understand the causes and implications of an extinction event, detailed information is necessary. However, this can be challenging when working with poorly resolved paleontological data sets. One approach to increase the data resolution is by combining different methods. In this study, we used both radiocarbon and genetic data to reconstruct the population history and extinction dynamics of the woolly mammoth in northern Siberia. We generated 88 new radiocarbon dates and combined these with previously published dates from 626 specimens to construct Bayesian age models. These models show that mammoths disappeared on the eastern Siberian mainland before the onset of the Younger Dryas (12.9–11.7 ky cal BP). Mammoths did however persist in the northernmost parts of central and western Siberia until the early Holocene. Further genetic results of 131 high quality mitogenomes, including 22 new mitogenomes generated in this study, support the hypothesis that mammoths from, or closely related to, a central and/or west- Siberian population recolonized Wrangel Island over the now submerged northern Siberian plains. As mammoths became trapped on the island due to rising sea levels, they lived another ca. 6000 years on Wrangel Island before eventually going extinct ca. 4000 years ago.
Published: 2021

23. Arctic-adapted dogs emerged at the Pleistocene-Holocene transitiond

Author: Sinding, Mikkel-Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmin, de Manuel, Marc, Pitulko, Vladimir V., Kuderna, Lukas, Feuerborn, Tatiana R., Frantz, Laurent A. F., Vieira, Filipe G., Niemann, Jonas, Castruita, Jose A. Samaniego, Caroe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jorgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalen, Love, Larson, Greger, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Oystein, Marques-Bonet, Tomas, Hansen, Anders J., Gilbert, M. Thomas P., Sinding, Mikkel-Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmin, de Manuel, Marc, Pitulko, Vladimir V., Kuderna, Lukas, Feuerborn, Tatiana R., Frantz, Laurent A. F., Vieira, Filipe G., Niemann, Jonas, Castruita, Jose A. Samaniego, Caroe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jorgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalen, Love, Larson, Greger, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Oystein, Marques-Bonet, Tomas, Hansen, Anders J., and Gilbert, M. Thomas P.
Abstract: Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an similar to 9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an similar to 33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
Published: 2020
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24. Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Author: Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel Holger S., Schuenemann, Verena J., Perri, Angela, Germonpré, Mietje, Bocherens, Hervé, Witt, Kelsey E., Samaniego Castruita, Jose A., Velasco, Marcela S., Lundstrøm, Inge K.C., Wales, Nathan, Sonet, Gontran, Frantz, Laurent, Schroeder, Hannes, Budd, Jane, Jimenez, Elodie Laure, Fedorov, Sergey, Gasparyan, Boris, Kandel, Andrew W., Lázničková-Galetová, Martina, Napierala, Hannes, Uerpmann, Hans Peter, Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir V., Herzig, Karl-Heinz, Malhi, Ripan S., Willerslev, Eske, Hansen, Anders J., Dobney, Keith, Gilbert, M. Thomas P., Krause, Johannes, Larson, Greger, Eriksson, Anders, Manica, Andrea, Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel Holger S., Schuenemann, Verena J., Perri, Angela, Germonpré, Mietje, Bocherens, Hervé, Witt, Kelsey E., Samaniego Castruita, Jose A., Velasco, Marcela S., Lundstrøm, Inge K.C., Wales, Nathan, Sonet, Gontran, Frantz, Laurent, Schroeder, Hannes, Budd, Jane, Jimenez, Elodie Laure, Fedorov, Sergey, Gasparyan, Boris, Kandel, Andrew W., Lázničková-Galetová, Martina, Napierala, Hannes, Uerpmann, Hans Peter, Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir V., Herzig, Karl-Heinz, Malhi, Ripan S., Willerslev, Eske, Hansen, Anders J., Dobney, Keith, Gilbert, M. Thomas P., Krause, Johannes, Larson, Greger, Eriksson, Anders, and Manica, Andrea
Abstract: Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
Published: 2020

25. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Author: Sinding, Mikkel-Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir, Kuderna, Lukas, Feuerborn, Tatiana, Frantz, Laurent, Garrett Vieira, Filipe, Niemann, Jonas, Samaniego Castruita, José Alfredo, Carøe, Christian, Andersen-Ranberg, Emilie Ulrikka, Jordan, Peter, Pavlova, Elena, Nikolskiy, Pavel, Kasparov, Aleksei, Ivanova, Varvara, Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders Johannes, Gilbert, M. Thomas P., Sinding, Mikkel-Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir, Kuderna, Lukas, Feuerborn, Tatiana, Frantz, Laurent, Garrett Vieira, Filipe, Niemann, Jonas, Samaniego Castruita, José Alfredo, Carøe, Christian, Andersen-Ranberg, Emilie Ulrikka, Jordan, Peter, Pavlova, Elena, Nikolskiy, Pavel, Kasparov, Aleksei, Ivanova, Varvara, Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders Johannes, and Gilbert, M. Thomas P.
Abstract: Altres ajuts: Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B01111), Obra Social "La Caixa", Natural Environmental Research Council (Grants NE/K005243/1 and NE/K003259/1), Francis Crick Institute (FC001595), Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
Published: 2020

26. Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Author: Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel Holger S., Schuenemann, Verena J., Perri, Angela, Germonpré, Mietje, Bocherens, Hervé, Witt, Kelsey E., Samaniego Castruita, Jose A., Velasco, Marcela S., Lundstrøm, Inge K.C., Wales, Nathan, Sonet, Gontran, Frantz, Laurent, Schroeder, Hannes, Budd, Jane, Jimenez, Elodie Laure, Fedorov, Sergey, Gasparyan, Boris, Kandel, Andrew W., Lázničková-Galetová, Martina, Napierala, Hannes, Uerpmann, Hans Peter, Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir V., Herzig, Karl-Heinz, Malhi, Ripan S., Willerslev, Eske, Hansen, Anders J., Dobney, Keith, Gilbert, M. Thomas P., Krause, Johannes, Larson, Greger, Eriksson, Anders, Manica, Andrea, Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel Holger S., Schuenemann, Verena J., Perri, Angela, Germonpré, Mietje, Bocherens, Hervé, Witt, Kelsey E., Samaniego Castruita, Jose A., Velasco, Marcela S., Lundstrøm, Inge K.C., Wales, Nathan, Sonet, Gontran, Frantz, Laurent, Schroeder, Hannes, Budd, Jane, Jimenez, Elodie Laure, Fedorov, Sergey, Gasparyan, Boris, Kandel, Andrew W., Lázničková-Galetová, Martina, Napierala, Hannes, Uerpmann, Hans Peter, Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir V., Herzig, Karl-Heinz, Malhi, Ripan S., Willerslev, Eske, Hansen, Anders J., Dobney, Keith, Gilbert, M. Thomas P., Krause, Johannes, Larson, Greger, Eriksson, Anders, and Manica, Andrea
Abstract: Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
Published: 2020

27. Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Author: Ramos-Madrigal, Jazmín, Sinding, Mikkel-Holger S, Carøe, Christian, Mak, Sarah S T, Niemann, Jonas, Samaniego Castruita, José A, Fedorov, Sergey, Kandyba, Alexander, Germonpré, Mietje, Bocherens, Hervé, Feuerborn, Tatiana R, Pitulko, Vladimir V, Pavlova, Elena Y, Nikolskiy, Pavel A, Kasparov, Aleksei K, Ivanova, Varvara V, Larson, Greger, Frantz, Laurent A F, Willerslev, Eske, Meldgaard, Morten, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Hansen, Anders J, Gilbert, M Thomas P, Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, Sinding, Mikkel-Holger S, Carøe, Christian, Mak, Sarah S T, Niemann, Jonas, Samaniego Castruita, José A, Fedorov, Sergey, Kandyba, Alexander, Germonpré, Mietje, Bocherens, Hervé, Feuerborn, Tatiana R, Pitulko, Vladimir V, Pavlova, Elena Y, Nikolskiy, Pavel A, Kasparov, Aleksei K, Ivanova, Varvara V, Larson, Greger, Frantz, Laurent A F, Willerslev, Eske, Meldgaard, Morten, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Hansen, Anders J, Gilbert, M Thomas P, and Gopalakrishnan, Shyam
Abstract: Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
Published: 2020

28. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Author: Sinding, Mikkel Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir V., Kuderna, Lukas, Feuerborn, Tatiana R., Frantz, Laurent A.F., Vieira, Filipe G., Niemann, Jonas, Samaniego Castruita, Jose A., Carøe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders J., Gilbert, M. Thomas P., Sinding, Mikkel Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir V., Kuderna, Lukas, Feuerborn, Tatiana R., Frantz, Laurent A.F., Vieira, Filipe G., Niemann, Jonas, Samaniego Castruita, Jose A., Carøe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders J., and Gilbert, M. Thomas P.
Abstract: Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
Published: 2020

29. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Author: Velux Foundation, European Commission, Independent Research Fund Denmark, Carlsberg Foundation, Generalitat de Catalunya, European Research Council, Natural Environment Research Council (UK), Russian Science Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación la Caixa, Howard Hughes Medical Institute, Sinding, Mikkel-Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, Manuel, Marc de, Pitulko, Vladimir, Kuderna, Lukas F. K., Feuerborn, Tatiana R., Frantz, Laurent A. F., Vieira, Filipe Garrett, Niemann, Jonas, Samaniego Castruita, José Alfredo, Carøe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei, Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Marqués-Bonet, Tomàs, Hansen, Anders J., Gilbert, M. Thomas P., Velux Foundation, European Commission, Independent Research Fund Denmark, Carlsberg Foundation, Generalitat de Catalunya, European Research Council, Natural Environment Research Council (UK), Russian Science Foundation, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación la Caixa, Howard Hughes Medical Institute, Sinding, Mikkel-Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, Manuel, Marc de, Pitulko, Vladimir, Kuderna, Lukas F. K., Feuerborn, Tatiana R., Frantz, Laurent A. F., Vieira, Filipe Garrett, Niemann, Jonas, Samaniego Castruita, José Alfredo, Carøe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei, Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Marqués-Bonet, Tomàs, Hansen, Anders J., and Gilbert, M. Thomas P.
Abstract: Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
Published: 2020

30. Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Author: Ramos-Madrigal, Jazmín, Sinding, Mikkel-Holger S, Carøe, Christian, Mak, Sarah S T, Niemann, Jonas, Samaniego Castruita, José A, Fedorov, Sergey, Kandyba, Alexander, Germonpré, Mietje, Bocherens, Hervé, Feuerborn, Tatiana R, Pitulko, Vladimir V, Pavlova, Elena Y, Nikolskiy, Pavel A, Kasparov, Aleksei K, Ivanova, Varvara V, Larson, Greger, Frantz, Laurent A F, Willerslev, Eske, Meldgaard, Morten, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Hansen, Anders J, Gilbert, M Thomas P, Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, Sinding, Mikkel-Holger S, Carøe, Christian, Mak, Sarah S T, Niemann, Jonas, Samaniego Castruita, José A, Fedorov, Sergey, Kandyba, Alexander, Germonpré, Mietje, Bocherens, Hervé, Feuerborn, Tatiana R, Pitulko, Vladimir V, Pavlova, Elena Y, Nikolskiy, Pavel A, Kasparov, Aleksei K, Ivanova, Varvara V, Larson, Greger, Frantz, Laurent A F, Willerslev, Eske, Meldgaard, Morten, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Hansen, Anders J, Gilbert, M Thomas P, and Gopalakrishnan, Shyam
Abstract: Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
Published: 2020

31. Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia

Author: Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel Holger S., Schuenemann, Verena J., Perri, Angela, Germonpré, Mietje, Bocherens, Hervé, Witt, Kelsey E., Samaniego Castruita, Jose A., Velasco, Marcela S., Lundstrøm, Inge K.C., Wales, Nathan, Sonet, Gontran, Frantz, Laurent, Schroeder, Hannes, Budd, Jane, Jimenez, Elodie Laure, Fedorov, Sergey, Gasparyan, Boris, Kandel, Andrew W., Lázničková-Galetová, Martina, Napierala, Hannes, Uerpmann, Hans Peter, Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir V., Herzig, Karl-Heinz, Malhi, Ripan S., Willerslev, Eske, Hansen, Anders J., Dobney, Keith, Gilbert, M. Thomas P., Krause, Johannes, Larson, Greger, Eriksson, Anders, Manica, Andrea, Loog, Liisa, Thalmann, Olaf, Sinding, Mikkel Holger S., Schuenemann, Verena J., Perri, Angela, Germonpré, Mietje, Bocherens, Hervé, Witt, Kelsey E., Samaniego Castruita, Jose A., Velasco, Marcela S., Lundstrøm, Inge K.C., Wales, Nathan, Sonet, Gontran, Frantz, Laurent, Schroeder, Hannes, Budd, Jane, Jimenez, Elodie Laure, Fedorov, Sergey, Gasparyan, Boris, Kandel, Andrew W., Lázničková-Galetová, Martina, Napierala, Hannes, Uerpmann, Hans Peter, Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir V., Herzig, Karl-Heinz, Malhi, Ripan S., Willerslev, Eske, Hansen, Anders J., Dobney, Keith, Gilbert, M. Thomas P., Krause, Johannes, Larson, Greger, Eriksson, Anders, and Manica, Andrea
Abstract: Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
Published: 2020

32. The population history of northeastern Siberia since the Pleistocene.

Author: Sikora, Martin, Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, Willerslev, Eske, Sikora, Martin, Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske
Abstract: Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
Published: 2019

33. The population history of northeastern Siberia since the Pleistocene.

Author: Sikora, Martin, Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, Willerslev, Eske, Sikora, Martin, Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske
Abstract: Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
Published: 2019

34. The population history of northeastern Siberia since the Pleistocene

Author: Sikora, Martin, Pitulko, Vladimir V., Sousa, Vitor C., Allentoft, Morten E., Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A., Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V., Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y., Chasnyk, Vyacheslav G., Nikolskiy, Pavel A., Gromov, Andrei V., Khartanovich, Valeriy I., Moiseyev, Vyacheslav, Grebenyuk, Pavel S., Fedorchenko, Alexander Yu, Lebedintsev, Alexander I., Slobodin, Sergey B., Malyarchuk, Boris A., Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U., Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S., Sjögren, Karl Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J., Excoffier, Laurent, Willerslev, Eske, Sikora, Martin, Pitulko, Vladimir V., Sousa, Vitor C., Allentoft, Morten E., Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A., Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V., Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y., Chasnyk, Vyacheslav G., Nikolskiy, Pavel A., Gromov, Andrei V., Khartanovich, Valeriy I., Moiseyev, Vyacheslav, Grebenyuk, Pavel S., Fedorchenko, Alexander Yu, Lebedintsev, Alexander I., Slobodin, Sergey B., Malyarchuk, Boris A., Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U., Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S., Sjögren, Karl Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J., Excoffier, Laurent, and Willerslev, Eske
Abstract: Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
Published: 2019

35. The population history of northeastern Siberia since the Pleistocene

Author: Sikora, Martin, Pitulko, Vladimir V., Sousa, Vitor C., Allentoft, Morten E., Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, Damgaard, Peter de Barros, de la Fuente Castro, Constanza, Renaud, Gabriel, Yang, Melinda A., Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogues, David Bravo, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V., Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y., Chasnyk, Vyacheslav G., Nikolskiy, Pavel A., Gromov, Andrei V., Khartanovich, Valeriy I., Moiseyev, Vyacheslav, Grebenyuk, Pavel S., Fedorchenko, Alexander Yu, Lebedintsev, Alexander I., Slobodin, Sergey B., Malyarchuk, Boris A., Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U., Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S., Sjögren, Karl Göran, Nielsen, Rasmus, Willerslev, Eske, Sikora, Martin, Pitulko, Vladimir V., Sousa, Vitor C., Allentoft, Morten E., Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, Damgaard, Peter de Barros, de la Fuente Castro, Constanza, Renaud, Gabriel, Yang, Melinda A., Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogues, David Bravo, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V., Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y., Chasnyk, Vyacheslav G., Nikolskiy, Pavel A., Gromov, Andrei V., Khartanovich, Valeriy I., Moiseyev, Vyacheslav, Grebenyuk, Pavel S., Fedorchenko, Alexander Yu, Lebedintsev, Alexander I., Slobodin, Sergey B., Malyarchuk, Boris A., Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U., Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S., Sjögren, Karl Göran, Nielsen, Rasmus, and Willerslev, Eske
Abstract: Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
Published: 2019

36. The evolutionary history of dogs in the Americas

Author: Leathlobhair, Maire Ni, Perri, Angela R., Irving-Pease, Evan K., Witt, Kelsey E., Linderholm, Anna, Haile, James, Lebrasseur, Ophelie, Ameen, Carly, Blick, Jeffrey, Boyko, Adam R., Brace, Selina, Cortes, Yahaira Nunes, Crockford, Susan J., Devault, Alison, Dimopoulos, Evangelos A., Eldridge, Morley, Enk, Jacob, Gopalakrishnan, Shyam, Gori, Kevin, Grimes, Vaughan, Guiry, Eric, Hansen, Anders Johannes, Hulme-Beaman, Ardern, Johnson, John, Kitchen, Andrew, Kasparov, Aleksei K., Kwon, Young-Mi, Nikolskiy, Pavel A., Lope, Carlos Peraza, Manin, Aurélie, Martin, Terrance, Meyer, Michael, Myers, Kelsey Noack, Omura, Mark, Rouillard, Jean-Marie, Pavlova, Elena Y., Sciulli, Paul, Sinding, Mikkel-Holger S., Strakova, Andrea, Ivanova, Varvara V., Widga, Christopher, Willerslev, Eske, Pitulko, Vladimir V., Barnes, Ian, Gilbert, M. Thomas P., Dobney, Keith M., Malhi, Ripan S., Murchison, Elizabeth P., Larson, Greger, Frantz, Laurent A. F., Leathlobhair, Maire Ni, Perri, Angela R., Irving-Pease, Evan K., Witt, Kelsey E., Linderholm, Anna, Haile, James, Lebrasseur, Ophelie, Ameen, Carly, Blick, Jeffrey, Boyko, Adam R., Brace, Selina, Cortes, Yahaira Nunes, Crockford, Susan J., Devault, Alison, Dimopoulos, Evangelos A., Eldridge, Morley, Enk, Jacob, Gopalakrishnan, Shyam, Gori, Kevin, Grimes, Vaughan, Guiry, Eric, Hansen, Anders Johannes, Hulme-Beaman, Ardern, Johnson, John, Kitchen, Andrew, Kasparov, Aleksei K., Kwon, Young-Mi, Nikolskiy, Pavel A., Lope, Carlos Peraza, Manin, Aurélie, Martin, Terrance, Meyer, Michael, Myers, Kelsey Noack, Omura, Mark, Rouillard, Jean-Marie, Pavlova, Elena Y., Sciulli, Paul, Sinding, Mikkel-Holger S., Strakova, Andrea, Ivanova, Varvara V., Widga, Christopher, Willerslev, Eske, Pitulko, Vladimir V., Barnes, Ian, Gilbert, M. Thomas P., Dobney, Keith M., Malhi, Ripan S., Murchison, Elizabeth P., Larson, Greger, and Frantz, Laurent A. F.
Published: 2018

37. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Author: Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, Dalén, Love, Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, and Dalén, Love
Published: 2017
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38. Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth

Author: Pecnerova, Patricia, Diez-del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, Dalen, Love, Pecnerova, Patricia, Diez-del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, and Dalen, Love
Published: 2017
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39. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Author: Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, Dalén, Love, Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, and Dalén, Love
Published: 2017
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40. Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth

Author: Pecnerova, Patricia, Diez-del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, Dalen, Love, Pecnerova, Patricia, Diez-del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, and Dalen, Love
Published: 2017
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41. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size

Author: Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, Dalén, Love, Pečnerová, Patrícia, Palkopoulou, Eleftheria, Wheat, Christopher W., Skoglund, Pontus, Vartanyan, Sergey, Tikhonov, Alexei, Nikolskiy, Pavel, van der Plicht, Johannes, Díez-del-Molino, David, and Dalén, Love
Abstract: The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high-quality mitogenomes from 21 radiocarbon-dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.
Published: 2017
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42. Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth

Author: Pečnerová, Patrícia, Díez-Del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, Dalén, Love, Pečnerová, Patrícia, Díez-Del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, and Dalén, Love
Abstract: While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. Wehypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.
Published: 2017
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43. Genome-based sexing provides clues about behavior and social structure in the woolly mammoth

Author: Pečnerová, Patricia, Díez-del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana Richtman, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, Dalén, Love, Pečnerová, Patricia, Díez-del-Molino, David, Dussex, Nicolas, Feuerborn, Tatiana Richtman, von Seth, Johanna, van der Plicht, Johannes, Nikolskiy, Pavel, Tikhonov, Alexei, Vartanyan, Sergey, and Dalén, Love
Published: 2017

44. Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings

Author: Palkopoulou, Eleftheria, Baca, Mateusz, Abramson, Natalia I., Sablin, Mikhail, Socha, Pawel, Nadachowski, Adam, Prost, Stefan, Germonpre, Mietje, Kosintsev, Pavel, Smirnov, Nickolay G., Vartanyan, Sergey, Ponomarev, Dmitry, Nystroem, Johanna, Nikolskiy, Pavel, Jass, Christopher N., Litvinov, Yuriy N., Kalthoff, Daniela C., Grigoriev, Semyon, Fadeeva, Tatyana, Douka, Aikaterini, Higham, Thomas F. G., Ersmark, Erik, Pitulko, Vladimir, Pavlova, Elena, Stewart, John R., Weglenski, Piotr, Stankovic, Anna, Dalen, Love, Palkopoulou, Eleftheria, Baca, Mateusz, Abramson, Natalia I., Sablin, Mikhail, Socha, Pawel, Nadachowski, Adam, Prost, Stefan, Germonpre, Mietje, Kosintsev, Pavel, Smirnov, Nickolay G., Vartanyan, Sergey, Ponomarev, Dmitry, Nystroem, Johanna, Nikolskiy, Pavel, Jass, Christopher N., Litvinov, Yuriy N., Kalthoff, Daniela C., Grigoriev, Semyon, Fadeeva, Tatyana, Douka, Aikaterini, Higham, Thomas F. G., Ersmark, Erik, Pitulko, Vladimir, Pavlova, Elena, Stewart, John R., Weglenski, Piotr, Stankovic, Anna, and Dalen, Love
Abstract: Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical his
Published: 2016
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45. Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings

Author: Palkopoulou, Eleftheria, Baca, Mateusz, Abramson, Natalia I., Sablin, Mikhail, Socha, Pawel, Nadachowski, Adam, Prost, Stefan, Germonpre, Mietje, Kosintsev, Pavel, Smirnov, Nickolay G., Vartanyan, Sergey, Ponomarev, Dmitry, Nystroem, Johanna, Nikolskiy, Pavel, Jass, Christopher N., Litvinov, Yuriy N., Kalthoff, Daniela C., Grigoriev, Semyon, Fadeeva, Tatyana, Douka, Aikaterini, Higham, Thomas F. G., Ersmark, Erik, Pitulko, Vladimir, Pavlova, Elena, Stewart, John R., Weglenski, Piotr, Stankovic, Anna, Dalen, Love, Palkopoulou, Eleftheria, Baca, Mateusz, Abramson, Natalia I., Sablin, Mikhail, Socha, Pawel, Nadachowski, Adam, Prost, Stefan, Germonpre, Mietje, Kosintsev, Pavel, Smirnov, Nickolay G., Vartanyan, Sergey, Ponomarev, Dmitry, Nystroem, Johanna, Nikolskiy, Pavel, Jass, Christopher N., Litvinov, Yuriy N., Kalthoff, Daniela C., Grigoriev, Semyon, Fadeeva, Tatyana, Douka, Aikaterini, Higham, Thomas F. G., Ersmark, Erik, Pitulko, Vladimir, Pavlova, Elena, Stewart, John R., Weglenski, Piotr, Stankovic, Anna, and Dalen, Love
Abstract: Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical his
Published: 2016
Full Text: View/download PDF

46. Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings

Author: Palkopoulou, Eleftheria, Baca, Mateusz, Abramson, Natalia I., Sablin, Mikhail, Socha, Pawel, Nadachowski, Adam, Prost, Stefan, Germonpre, Mietje, Kosintsev, Pavel, Smirnov, Nickolay G., Vartanyan, Sergey, Ponomarev, Dmitry, Nyström, Johanna, Nikolskiy, Pavel, Jass, Christopher N., Litvinov, Yuriy N., Kalthoff, Daniela C., Grigoriev, Semyon, Fadeeva, Tatyana, Douka, Aikaterini, Higham, Thomas F. G., Ersmark, Erik, Pitulko, Vladimir, Pavlova, Elena, Stewart, John R., Weglenski, Piotr, Stankovic, Anna, Dalén, Love, Palkopoulou, Eleftheria, Baca, Mateusz, Abramson, Natalia I., Sablin, Mikhail, Socha, Pawel, Nadachowski, Adam, Prost, Stefan, Germonpre, Mietje, Kosintsev, Pavel, Smirnov, Nickolay G., Vartanyan, Sergey, Ponomarev, Dmitry, Nyström, Johanna, Nikolskiy, Pavel, Jass, Christopher N., Litvinov, Yuriy N., Kalthoff, Daniela C., Grigoriev, Semyon, Fadeeva, Tatyana, Douka, Aikaterini, Higham, Thomas F. G., Ersmark, Erik, Pitulko, Vladimir, Pavlova, Elena, Stewart, John R., Weglenski, Piotr, Stankovic, Anna, and Dalén, Love
Abstract: Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical his
Published: 2016
Full Text: View/download PDF

47. A MIS 3 Kill-Butchery Mammoth Site on Buor-Khaya Penninsula, Eastern Laptev Sea, Russian Arctic

Author: Kostopoulos, Dimitris, Vlachos, Evangelos, Tsoukala, Evangelia, Pitulko, Vladimir, Yakshina, Irina, Strauss, Jens, Schirrmeister, Lutz, Kuznetsova, Tatyana, Nikolskiy, Pavel, Pavlova, Elena, Kostopoulos, Dimitris, Vlachos, Evangelos, Tsoukala, Evangelia, Pitulko, Vladimir, Yakshina, Irina, Strauss, Jens, Schirrmeister, Lutz, Kuznetsova, Tatyana, Nikolskiy, Pavel, and Pavlova, Elena
Abstract: An assemblage of Pleistocene faunal remains was collected by a field party of «Eastern Laptev Sea - Buor Khaya Peninsula» expedition (Strauss et al., 2011) from Orto-Stan River, Buor-Khaya Peninsula. The bones were sampled from a concentration located next to the edge of a thermokast lake (N 71° 36,120' E 132° 15,597'). Two mammoth bones with human impact and a horse bone were dated directly. The site age is estimated at 27,000 – 27,600 14C yrs BP, which corresponds to the end of MIS 3, or slightly older if the horse bone belongs to the same level. These dates indicate that the mammoth remains were accumulating for at least 500 years. Mammoth remains constitute two thirds of the yield. There are at least five mammoth individuals, both adults and juveniles. Two pelvic bones have identical blind holes near the coxofemoral articulation on the bones’ caudal sides., Bone cracks caused by such damage loosened the joint and facilitated disarticulation during the butchering process. Multiple lines engraved by sharp lithic tool are visible on caudal surface of a right pelvic bone. Lines are 1.2-2 mm wide and ~0.7 mm deep. Except for the butchery marks, the Buor-Khaya/Orto-Stan mammoth site provides evidence for killing these animals. Finds from Yana RHS site (Nikolskiy, Pitulko, 2013) suggest that people applied a «spear-fall» hunting strategy, similar to that practiced by African hunter-gatherers. For example, Kulik (1971) describes a specific coup de grâce method practiced by Pygmies to cut important arteries and cause mortal bleeding by trusting a spear into the elephant’s trunk . The position of the cut-marks on the edge of the nasal opening of the mammoth skull fragments at the Buor-Khaya/Orto-Stan, i.e. near the trunk, suggests that they were caused by the same action. Therefore, Buor-Khaya/Orto-Stan contains sufficient evidence to be accepted as a kill-butchery mammoth site, and currently the northernmost Paleolithic site in the world, which sheds light on human dispe
Published: 2014

48. A MIS 3 Kill-Butchery Mammoth Site on Buor-Khaya Penninsula, Eastern Laptev Sea, Russian Arctic

Author: Kostopoulos, Dimitris, Vlachos, Evangelos, Tsoukala, Evangelia, Pitulko, Vladimir, Yakshina, Irina, Strauss, Jens, Schirrmeister, Lutz, Kuznetsova, Tatyana, Nikolskiy, Pavel, Pavlova, Elena, Kostopoulos, Dimitris, Vlachos, Evangelos, Tsoukala, Evangelia, Pitulko, Vladimir, Yakshina, Irina, Strauss, Jens, Schirrmeister, Lutz, Kuznetsova, Tatyana, Nikolskiy, Pavel, and Pavlova, Elena
Abstract: An assemblage of Pleistocene faunal remains was collected by a field party of «Eastern Laptev Sea - Buor Khaya Peninsula» expedition (Strauss et al., 2011) from Orto-Stan River, Buor-Khaya Peninsula. The bones were sampled from a concentration located next to the edge of a thermokast lake (N 71° 36,120' E 132° 15,597'). Two mammoth bones with human impact and a horse bone were dated directly. The site age is estimated at 27,000 – 27,600 14C yrs BP, which corresponds to the end of MIS 3, or slightly older if the horse bone belongs to the same level. These dates indicate that the mammoth remains were accumulating for at least 500 years. Mammoth remains constitute two thirds of the yield. There are at least five mammoth individuals, both adults and juveniles. Two pelvic bones have identical blind holes near the coxofemoral articulation on the bones’ caudal sides., Bone cracks caused by such damage loosened the joint and facilitated disarticulation during the butchering process. Multiple lines engraved by sharp lithic tool are visible on caudal surface of a right pelvic bone. Lines are 1.2-2 mm wide and ~0.7 mm deep. Except for the butchery marks, the Buor-Khaya/Orto-Stan mammoth site provides evidence for killing these animals. Finds from Yana RHS site (Nikolskiy, Pitulko, 2013) suggest that people applied a «spear-fall» hunting strategy, similar to that practiced by African hunter-gatherers. For example, Kulik (1971) describes a specific coup de grâce method practiced by Pygmies to cut important arteries and cause mortal bleeding by trusting a spear into the elephant’s trunk . The position of the cut-marks on the edge of the nasal opening of the mammoth skull fragments at the Buor-Khaya/Orto-Stan, i.e. near the trunk, suggests that they were caused by the same action. Therefore, Buor-Khaya/Orto-Stan contains sufficient evidence to be accepted as a kill-butchery mammoth site, and currently the northernmost Paleolithic site in the world, which sheds light on human dispe
Published: 2014

49. The first record of 'spelaeoid' bears in Arctic Siberia

Author: Sher, Andrei V., Weinstock Arenovitz, Jacobo, Baryshnikov, Gennady F., Davydov, Sergey P., Boeskorov, Gennady G., Zazhigin, Vladimir S., Nikolskiy, Pavel A., Sher, Andrei V., Weinstock Arenovitz, Jacobo, Baryshnikov, Gennady F., Davydov, Sergey P., Boeskorov, Gennady G., Zazhigin, Vladimir S., and Nikolskiy, Pavel A.
Published: 2011

50. The first record of 'spelaeoid' bears in Arctic Siberia

Author: Sher, Andrei V., Weinstock Arenovitz, Jacobo, Baryshnikov, Gennady F., Davydov, Sergey P., Boeskorov, Gennady G., Zazhigin, Vladimir S., Nikolskiy, Pavel A., Sher, Andrei V., Weinstock Arenovitz, Jacobo, Baryshnikov, Gennady F., Davydov, Sergey P., Boeskorov, Gennady G., Zazhigin, Vladimir S., and Nikolskiy, Pavel A.
Published: 2011

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