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

Author

Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. -H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C., Swali, P., Conard, N. J., Carøe, C., Haile, J., Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, A. J., Willerslev, E., Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M. T. P., Shapiro, B., Larson, G., Krause, J., Dalén, L., Skoglund, P., Bergström, A., Stanton, D. W. G., Taron, U. H., Frantz, L., Sinding, M. -H. S., Ersmark, E., Pfrengle, S., Cassatt-Johnstone, M., Lebrasseur, O., Girdland-Flink, L., Fernandes, D. M., Ollivier, M., Speidel, L., Gopalakrishnan, S., Westbury, M. V., Ramos-Madrigal, J., Feuerborn, T. R., Reiter, E., Gretzinger, J., Münzel, S. C., Swali, P., Conard, N. J., Carøe, C., Haile, J., Linderholm, A., Androsov, S., Barnes, I., Baumann, C., Benecke, N., Bocherens, H., Brace, S., Carden, R. F., Drucker, D. G., Fedorov, S., Gasparik, M., Germonpré, M., Grigoriev, S., Groves, P., Hertwig, S. T., Ivanova, V. V., Janssens, L., Jennings, R. P., Kasparov, A. K., Kirillova, I. V., Kurmaniyazov, I., Kuzmin, Y. V., Kosintsev, P. A., Lázničková-Galetová, M., Leduc, C., Nikolskiy, P., Nussbaumer, M., O’Drisceoil, C., Orlando, L., Outram, A., Pavlova, E. Y., Perri, A. R., Pilot, M., Pitulko, V. V., Plotnikov, V. V., Protopopov, A. V., Rehazek, A., Sablin, M., Seguin-Orlando, A., Storå, J., Verjux, C., Zaibert, V. F., Zazula, G., Crombé, P., Hansen, A. J., Willerslev, E., Leonard, J. A., Götherström, A., Pinhasi, R., Schuenemann, V. J., Hofreiter, M., Gilbert, M. T. P., Shapiro, B., Larson, G., Krause, J., Dalén, L., and Skoglund, P.

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. © 2022, The Author(s).

Published
2022

5. Ancient and Modern Genomes Unravel the Evolutionary History of the Rhinoceros Family

Author

Liu, S., Westbury, M. V., Dussex, N., Mitchell, K. J., Sinding, M. -H. S., Heintzman, P. D., Duchêne, D. A., Kapp, J. D., von Seth, J., Heiniger, H., Sánchez-Barreiro, F., Margaryan, A., André-Olsen, R., De Cahsan, B., Meng, G., Yang, C., Chen, L., van der Valk, T., Moodley, Y., Rookmaaker, K., Bruford, M. W., Ryder, O., Steiner, C., Bruins-van Sonsbeek, L. G. R., Vartanyan, S., Guo, C., Cooper, A., Kosintsev, P., Kirillova, I., Lister, A. M., Marques-Bonet, T., Gopalakrishnan, S., Dunn, R. R., Lorenzen, E. D., Shapiro, B., Zhang, G., Antoine, P. -O., Dalén, L., Gilbert, M. T. P., Liu, S., Westbury, M. V., Dussex, N., Mitchell, K. J., Sinding, M. -H. S., Heintzman, P. D., Duchêne, D. A., Kapp, J. D., von Seth, J., Heiniger, H., Sánchez-Barreiro, F., Margaryan, A., André-Olsen, R., De Cahsan, B., Meng, G., Yang, C., Chen, L., van der Valk, T., Moodley, Y., Rookmaaker, K., Bruford, M. W., Ryder, O., Steiner, C., Bruins-van Sonsbeek, L. G. R., Vartanyan, S., Guo, C., Cooper, A., Kosintsev, P., Kirillova, I., Lister, A. M., Marques-Bonet, T., Gopalakrishnan, S., Dunn, R. R., Lorenzen, E. D., Shapiro, B., Zhang, G., Antoine, P. -O., Dalén, L., and Gilbert, M. T. P.

Abstract

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines. © 2021 The Authors.

Published
2021

6. Dire Wolves Were the Last of an Ancient New World Canid Lineage

Author

Perri, A. R., Mitchell, K. J., Mouton, A., Álvarez-Carretero, S., Hulme-Beaman, A., Haile, J., Jamieson, A., Meachen, J., Lin, A. T., Schubert, B. W., Ameen, C., Antipina, E. E., Bover, P., Brace, S., Carmagnini, A., Carøe, C., Samaniego Castruita, J. A., Chatters, J. C., Dobney, K., dos Reis, M., Evin, A., Gaubert, P., Gopalakrishnan, S., Gower, G., Heiniger, H., Helgen, K. M., Kapp, J., Kosintsev, P. A., Linderholm, A., Ozga, A. T., Presslee, S., Salis, A. T., Saremi, N. F., Shew, C., Skerry, K., Taranenko, D. E., Thompson, M., Sablin, M. V., Kuzmin, Y. V., Collins, M. J., Sinding, M. -H. S., Gilbert, M. T. P., Stone, A. C., Shapiro, B., Van Valkenburgh, B., Wayne, R. K., Larson, G., Cooper, A., Frantz, L. A. F., Perri, A. R., Mitchell, K. J., Mouton, A., Álvarez-Carretero, S., Hulme-Beaman, A., Haile, J., Jamieson, A., Meachen, J., Lin, A. T., Schubert, B. W., Ameen, C., Antipina, E. E., Bover, P., Brace, S., Carmagnini, A., Carøe, C., Samaniego Castruita, J. A., Chatters, J. C., Dobney, K., dos Reis, M., Evin, A., Gaubert, P., Gopalakrishnan, S., Gower, G., Heiniger, H., Helgen, K. M., Kapp, J., Kosintsev, P. A., Linderholm, A., Ozga, A. T., Presslee, S., Salis, A. T., Saremi, N. F., Shew, C., Skerry, K., Taranenko, D. E., Thompson, M., Sablin, M. V., Kuzmin, Y. V., Collins, M. J., Sinding, M. -H. S., Gilbert, M. T. P., Stone, A. C., Shapiro, B., Van Valkenburgh, B., Wayne, R. K., Larson, G., Cooper, A., and Frantz, L. A. F.

Abstract

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently. © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

Published
2021

7. Modern Siberian Dog Ancestry was Shaped by Several Thousand Years of Eurasian-Wide Trade and Human Dispersal

Author

Feuerborn, T. R., Carmagnini, A., Losey, R. J., Nomokonova, T., Askeyev, A., Askeyev, I., Askeyev, O., Antipina, E. E., Appelt, M., Bachura, O. P., Beglane, F., Bradley, D. G., Daly, K. G., Gopalakrishnan, S., Gregersen, K. M., Guo, C., Gusev, A. V., Jones, C., Kosintsev, P. A., Kuzmin, Y. V., Mattiangeli, V., Perri, A. R., Plekhanov, A. V., Ramos-Madrigal, J., Schmidt, A. L., Shaymuratova, D., Smith, O., Yavorskaya, L. V., Zhang, G., Willerslev, E., Meldgaard, M., Gilbert, M. T. P., Larson, G., Dalén, L., Hansen, A. J., Sinding, M. -H. S., Frantz, L., Feuerborn, T. R., Carmagnini, A., Losey, R. J., Nomokonova, T., Askeyev, A., Askeyev, I., Askeyev, O., Antipina, E. E., Appelt, M., Bachura, O. P., Beglane, F., Bradley, D. G., Daly, K. G., Gopalakrishnan, S., Gregersen, K. M., Guo, C., Gusev, A. V., Jones, C., Kosintsev, P. A., Kuzmin, Y. V., Mattiangeli, V., Perri, A. R., Plekhanov, A. V., Ramos-Madrigal, J., Schmidt, A. L., Shaymuratova, D., Smith, O., Yavorskaya, L. V., Zhang, G., Willerslev, E., Meldgaard, M., Gilbert, M. T. P., Larson, G., Dalén, L., Hansen, A. J., Sinding, M. -H. S., and Frantz, L.

Abstract

Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Northwest Siberia around 2,000 y ago. It is unclear if the Siberian Arctic dog population was as continuous as the people of the region or if instead admixture occurred, possibly in relation to the influx of material culture from other parts of Eurasia. To address this question, we sequenced and analyzed the genomes of 20 ancient and historical Siberian and Eurasian Steppe dogs. Our analyses indicate that while Siberian dogs were genetically homogenous between 9,500 to 7,000 y ago, later introduction of dogs from the Eurasian Steppe and Europe led to substantial admixture. This is clearly the case in the Iamal-Nenets region (Northwestern Siberia) where dogs from the Iron Age period (∼2,000 y ago) possess substantially less ancestry related to European and Steppe dogs than dogs from the medieval period (∼1,000 y ago). Combined with findings of nonlocal materials recovered from these archaeological sites, including glass beads and metal items, these results indicate that Northwest Siberian communities were connected to a larger trade network through which they acquired genetically distinctive dogs from other regions. These exchanges were part of a series of major societal changes, including the rise of large-scale reindeer pastoralism ∼800 y ago. © 2021 National Academy of Sciences. All rights reserved.

Published
2021

8. African and Asian leopards are highly differentiated at the genomic level

Author

Paijmans, J L A, Barlow, A, Becker, M S, Cahill, J A, Fickel, J, Forster, D W G, Gries, K, Hartmann, S, Havmoller, R W, Henneberger, K, Kern, C, Kitchener, A C, Lorenzen, E D, Mayer, F, OBrien, S J, von Seth, J, Sinding, M H S, Spong, G, Uphyrkina, O, Wachter, B, Westbury, M V, Dalen, L, Bhak, J, Manica, A, Hofreiter, M, Paijmans, J L A, Barlow, A, Becker, M S, Cahill, J A, Fickel, J, Forster, D W G, Gries, K, Hartmann, S, Havmoller, R W, Henneberger, K, Kern, C, Kitchener, A C, Lorenzen, E D, Mayer, F, OBrien, S J, von Seth, J, Sinding, M H S, Spong, G, Uphyrkina, O, Wachter, B, Westbury, M V, Dalen, L, Bhak, J, Manica, A, and Hofreiter, M

Published
2021
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9. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations

Author

von Seth, J, Dussex, N, Diez-del-Molino, D, van der Valk, T, Kutschera, V E, Kierczak, M, Steiner, C C, Liu, S L, Gilbert, M T P, Sinding, M H S, Prost, S, Guschanski, K, Nathan, S K S S, Brace, S, Chan, Y L, Wheat, C W, Skoglund, P, Ryder, O A, Goossens, B, Gotherstrom, A, Dalen, L, von Seth, J, Dussex, N, Diez-del-Molino, D, van der Valk, T, Kutschera, V E, Kierczak, M, Steiner, C C, Liu, S L, Gilbert, M T P, Sinding, M H S, Prost, S, Guschanski, K, Nathan, S K S S, Brace, S, Chan, Y L, Wheat, C W, Skoglund, P, Ryder, O A, Goossens, B, Gotherstrom, A, and Dalen, L

Published
2021
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10. Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal

Author

Feuerborn, T R, Carmagnini, A, Losey, R J, Nomokonova, T, Askeyev, A, Askeyev, I, Askeyev, O, Antipina, E E, Appelt, M, Bachura, O P, Beglane, F, Bradley, D G, Daly, K G, Gopalakrishnan, S, Gregersen, K M, Guo, C X, Gusev, A V, Jones, C, Kosintsev, P A, Kuzmin, Y V, Mattiangeli, V, Perri, A R, Plekhanov, A V, Ramos-Madrigal, J, Schmidt, A L, Shaymuratova, D, Smith, O, Yavorskaya, L V, Zhang, G J, Willerslev, E, Meldgaard, M, Gilbert, M T P, Larson, G, Dalen, L, Hansen, A J, Sinding, M H S, Frantz, L, Feuerborn, T R, Carmagnini, A, Losey, R J, Nomokonova, T, Askeyev, A, Askeyev, I, Askeyev, O, Antipina, E E, Appelt, M, Bachura, O P, Beglane, F, Bradley, D G, Daly, K G, Gopalakrishnan, S, Gregersen, K M, Guo, C X, Gusev, A V, Jones, C, Kosintsev, P A, Kuzmin, Y V, Mattiangeli, V, Perri, A R, Plekhanov, A V, Ramos-Madrigal, J, Schmidt, A L, Shaymuratova, D, Smith, O, Yavorskaya, L V, Zhang, G J, Willerslev, E, Meldgaard, M, Gilbert, M T P, Larson, G, Dalen, L, Hansen, A J, Sinding, M H S, and Frantz, L

Published
2021
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11. Ancient and modem genomes unravel the evolutionary history of the rhinoceros family

Author

Liu, S L, Westbury, M V, Dussex, N, Mitchell, K J, Sinding, M H S, Heintzman, P D, Duchene, D A, Kapp, J D, von Seth, J, Heiniger, H, Sanchez-Barreiro, F, Margaryan, A, Andre-Olsen, R, De Cahsan, B, Meng, G L, Yang, C T, Chen, L, van der Valk, T, Moodley, Y, Rookmaaker, K, Bruford, M W, Ryder, O, Steiner, C, Bruins-van Sonsbeek, L G R, Vartanyan, S, Guo, C X, Cooper, A, Kosintsev, P, Kirillova, I, Lister, A M, Marques-Bonet, T, Gopalakrishnan, S, Dunn, R R, Lorenzen, E D, Shapiro, B, Zhang, G J, Antoine, P O, Dalen, L, Gilbert, M T P, Liu, S L, Westbury, M V, Dussex, N, Mitchell, K J, Sinding, M H S, Heintzman, P D, Duchene, D A, Kapp, J D, von Seth, J, Heiniger, H, Sanchez-Barreiro, F, Margaryan, A, Andre-Olsen, R, De Cahsan, B, Meng, G L, Yang, C T, Chen, L, van der Valk, T, Moodley, Y, Rookmaaker, K, Bruford, M W, Ryder, O, Steiner, C, Bruins-van Sonsbeek, L G R, Vartanyan, S, Guo, C X, Cooper, A, Kosintsev, P, Kirillova, I, Lister, A M, Marques-Bonet, T, Gopalakrishnan, S, Dunn, R R, Lorenzen, E D, Shapiro, B, Zhang, G J, Antoine, P O, Dalen, L, and Gilbert, M T P

Published
2021
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12. Stone Age 'chewing gum' yields 5,700 year-old human genome and oral microbiome

Author

Jensen, T. Z. T., Niemann, J., Iversen, K. Højholt, Fotakis, A.K., Gopalakrishnan, S., Sinding, M.­H. S., Ellegaard, M. R., Allentoft, M. E., Lanigan, L. T., Taurozzi, A. J., Nielsen, S. Holtsmark, Dee, M.W., Mortensen, M. N., Christensen, M. C., Sørensen, S. A., Collins, M. J., Gilbert, M.T.P., Sikora, M., Rasmussen, S., and Schroeder, H.

Subjects
Ancient DNA, Hunter-­gatherer, Microbial DNA, Neolithic, Resin, Mesolithic
Abstract

We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous “chewing gum” recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,858­5,661 cal. BP (GrM­13305; 5,007±11). We sequenced the genome to an average depth-­of­coverage of 2.3× and find that the individual who chewed the resin was female and genetically more closely related to western hunter­gatherers from mainland Europe, than hunter­gatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

Published
2019

13. Stone Age “chewing gum” yields 5,700 yearold human genome and oral microbiome

Author

Jensen, T. Z. T., Niemann, J., Iversen, K. Højholt, Fotaki, A. K., Gopalakrishan, S., Sinding, M.-H. S., Ellegaard, M. R., Allentoft, M. E., Lanigan, L. T., Taurozzi, A. J., Nielsen, S. Holtsmark, Dee, M. W., Mortensen, M. N., Christensen, M. C., Sørensen, S. A., Collins, M. J., Gilbert, M. T. P., Sikora, M., Rasmussen, S., Schroeder, H., Jensen, T. Z. T., Niemann, J., Iversen, K. Højholt, Fotaki, A. K., Gopalakrishan, S., Sinding, M.-H. S., Ellegaard, M. R., Allentoft, M. E., Lanigan, L. T., Taurozzi, A. J., Nielsen, S. Holtsmark, Dee, M. W., Mortensen, M. N., Christensen, M. C., Sørensen, S. A., Collins, M. J., Gilbert, M. T. P., Sikora, M., Rasmussen, S., and Schroeder, H.

Abstract

We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous “chewing gum” recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,8585,661 cal. BP (GrM13305; 5,007±1 1). We sequenced the genome to an average depthofcoverage of 2.3× and find that the individual who chewed the resin was female and genetically more closely related to western huntergatherers from mainland Europe, than huntergatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

Published
2018

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