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

Author

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

Subjects
Africa, Animals, DNA, Ancient, Dogs, Domestication, Europe, Genome, Genomics, History, Ancient, Middle East, Mutation, North America, Phylogeny, Selection, Genetic, Siberia, Tumor Suppressor Proteins, Wolves, General Science & Technology
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

2. Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids

Author

Plassais, Jocelyn, vonHoldt, Bridgett M, Parker, Heidi G, Carmagnini, Alberto, Dubos, Nicolas, Papa, Ilenia, Bevant, Kevin, Derrien, Thomas, Hennelly, Lauren M, Whitaker, D Thad, Harris, Alex C, Hogan, Andrew N, Huson, Heather J, Zaibert, Victor F, Linderholm, Anna, Haile, James, Fest, Thierry, Habib, Bilal, Sacks, Benjamin N, Benecke, Norbert, Outram, Alan K, Sablin, Mikhail V, Germonpré, Mietje, Larson, Greger, Frantz, Laurent, and Ostrander, Elaine A

Subjects
Biological Sciences, Genetics, Alleles, Animals, Body Size, Breeding, Canidae, Humans, Wolves, IGF1, ancient DNA, antisense lncRNA, body size, canid evolution, canine, dog, domestication, long non-coding RNA, wolf, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Published
2022

3. Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change.

Author

Seersholm, Frederik V, Werndly, Daniel J, Grealy, Alicia, Johnson, Taryn, Keenan Early, Erin M, Lundelius, Ernest L, Winsborough, Barbara, Farr, Grayal Earle, Toomey, Rickard, Hansen, Anders J, Shapiro, Beth, Waters, Michael R, McDonald, Gregory, Linderholm, Anna, Stafford, Thomas W, and Bunce, Michael

Abstract

Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.

Published
2020

4. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author

Ameen, Carly, Feuerborn, Tatiana R, Brown, Sarah K, Linderholm, Anna, Hulme-Beaman, Ardern, Lebrasseur, Ophélie, Sinding, Mikkel-Holger S, Lounsberry, Zachary T, Lin, Audrey T, Appelt, Martin, Bachmann, Lutz, Betts, Matthew, Britton, Kate, Darwent, John, Dietz, Rune, Fredholm, Merete, Gopalakrishnan, Shyam, Goriunova, Olga I, Grønnow, Bjarne, Haile, James, Hallsson, Jón Hallsteinn, Harrison, Ramona, Heide-Jørgensen, Mads Peter, Knecht, Rick, Losey, Robert J, Masson-MacLean, Edouard, McGovern, Thomas H, McManus-Fry, Ellen, Meldgaard, Morten, Midtdal, Åslaug, Moss, Madonna L, Nikitin, Iurii G, Nomokonova, Tatiana, Pálsdóttir, Albína Hulda, Perri, Angela, Popov, Aleksandr N, Rankin, Lisa, Reuther, Joshua D, Sablin, Mikhail, Schmidt, Anne Lisbeth, Shirar, Scott, Smiarowski, Konrad, Sonne, Christian, Stiner, Mary C, Vasyukov, Mitya, West, Catherine F, Ween, Gro Birgit, Wennerberg, Sanne Eline, Wiig, Øystein, Woollett, James, Dalén, Love, Hansen, Anders J, Gilbert, M Thomas P, Sacks, Benjamin N, Frantz, Laurent, Larson, Greger, Dobney, Keith, Darwent, Christyann M, and Evin, Allowen

Subjects
Biological Sciences, Genetics, Alaska, Animal Distribution, Animals, Archaeology, Arctic Regions, Canada, DNA, Ancient, DNA, Mitochondrial, Dogs, Genome, Mitochondrial, Greenland, Human Migration, Phenotype, archaeology, geometric morphometrics, ancient DNA, migration, Canis lupus familiaris, circumpolar, Agricultural and Veterinary Sciences, Medical and Health Sciences, Agricultural, veterinary and food sciences, Biological sciences, Environmental sciences
Abstract

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Published
2019

6. Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Author

Yu, He, Jamieson, Alexandra, Hulme-Beaman, Ardern, Conroy, Chris J., Knight, Becky, Speller, Camilla, Al-Jarah, Hiba, Eager, Heidi, Trinks, Alexandra, Adikari, Gamini, Baron, Henriette, Böhlendorf-Arslan, Beate, Bohingamuwa, Wijerathne, Crowther, Alison, Cucchi, Thomas, Esser, Kinie, Fleisher, Jeffrey, Gidney, Louisa, Gladilina, Elena, Gol’din, Pavel, Goodman, Steven M., Hamilton-Dyer, Sheila, Helm, Richard, Hillman, Jesse C., Kallala, Nabil, Kivikero, Hanna, Kovács, Zsófia E., Kunst, Günther Karl, Kyselý, René, Linderholm, Anna, Maraoui-Telmini, Bouthéina, Marković, Nemanja, Morales-Muñiz, Arturo, Nabais, Mariana, O’Connor, Terry, Oueslati, Tarek, Quintana Morales, Eréndira M., Pasda, Kerstin, Perera, Jude, Perera, Nimal, Radbauer, Silvia, Ramon, Joan, Rannamäe, Eve, Sanmartí Grego, Joan, Treasure, Edward, Valenzuela-Lamas, Silvia, van der Jagt, Inge, Van Neer, Wim, Vigne, Jean-Denis, Walker, Thomas, Wynne-Jones, Stephanie, Zeiler, Jørn, Dobney, Keith, Boivin, Nicole, Searle, Jeremy B., Krause-Kyora, Ben, Krause, Johannes, Larson, Greger, and Orton, David

Published
2022
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7. Synchronous diversification of Sulawesis iconic artiodactyls driven by recent geological events.

Author

Frantz, Laurent, Rudzinski, Anna, Nugraha, Abang, Evin, Allowen, Burton, James, Hulme-Beaman, Ardern, Linderholm, Anna, Barnett, Ross, Vega, Rodrigo, Irving-Pease, Evan, Haile, James, Allen, Richard, Leus, Kristin, Shephard, Jill, Hillyer, Mia, Gillemot, Sarah, van den Hurk, Jeroen, Ogle, Sharron, Atofanei, Cristina, Thomas, Mark, Johansson, Friederike, Mustari, Abdul, Williams, John, Mohamad, Kusdiantoro, Damayanti, Chandramaya, Wiryadi, Ita, Obbles, Dagmar, Mona, Stephano, Day, Hally, Yasin, Muhammad, Meker, Stefan, Evans, Ben, von Rintelen, Thomas, Ho, Simon, Searle, Jeremy, Kitchener, Andrew, Macdonald, Alastair, Shaw, Darren, Hall, Robert, Galbusera, Peter, Larson, Greger, and Mcguire, Jimmy

Subjects
Wallacea, biogeography, evolution, geology, Animals, Base Sequence, Buffaloes, DNA, Mitochondrial, Genetic Speciation, Geography, Geological Phenomena, Indonesia, Islands, Microsatellite Repeats, Phylogeny, Phylogeography, Swine
Abstract

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesis fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesis three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

Published
2018

9. Dire wolves were the last of an ancient New World canid lineage

Author

Perri, Angela R., Mitchell, Kieren J., Mouton, Alice, Álvarez-Carretero, Sandra, Hulme-Beaman, Ardern, Haile, James, Jamieson, Alexandra, Meachen, Julie, Lin, Audrey T., Schubert, Blaine W., Ameen, Carly, Antipina, Ekaterina E., Bover, Pere, Brace, Selina, Carmagnini, Alberto, Carøe, Christian, Samaniego Castruita, Jose A., Chatters, James C., Dobney, Keith, dos Reis, Mario, Evin, Allowen, Gaubert, Philippe, Gopalakrishnan, Shyam, Gower, Graham, Heiniger, Holly, Helgen, Kristofer M., Kapp, Josh, Kosintsev, Pavel A., Linderholm, Anna, Ozga, Andrew T., Presslee, Samantha, Salis, Alexander T., Saremi, Nedda F., Shew, Colin, Skerry, Katherine, Taranenko, Dmitry E., Thompson, Mary, Sablin, Mikhail V., Kuzmin, Yaroslav V., Collins, Matthew J., Sinding, Mikkel-Holger S., Gilbert, M. Thomas P., Stone, Anne C., Shapiro, Beth, Van Valkenburgh, Blaire, Wayne, Robert K., Larson, Greger, Cooper, Alan, and Frantz, Laurent A. F.

Published
2021
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10. Working Ethically with Ancient DNA from Composites in the United States.

Author

Johnson, Taryn, Thakar, Heather B., Watkins, Joe, and Linderholm, Anna

Subjects
FOSSIL DNA, DENTAL calculus, COPROLITES, RESEARCH ethics, ARCHAEOLOGISTS
Abstract

Copyright of Advances in Archaeological Practice is the property of Cambridge University Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2024
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11. Investigation of Submarine Groundwater Discharge into the Baltic Sea Through Varved Glacial Clays

Author

Chen, Nai-Chen, primary, O’Regan, Matt, additional, Hong, Wei-Li, additional, Andrén, Thomas, additional, Rodellas, Valentí, additional, Roth, Florian, additional, Mörth, Carl-Magnus, additional, Regnell, Carl, additional, Marxen, Hanna Sofia, additional, ten Hietbrink, Sophie, additional, Huang, Tzu-Hao, additional, Gyllencreautz, Richard, additional, Stranne, Christian, additional, Linderholm, Anna, additional, Garcia-Orellana, Jordi, additional, Humborg, Christoph, additional, and Jakobsson, Martin, additional

Published
2024
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12. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Bălăşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoğan, Aslı, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Fatemeh Mohaseb, Azadeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2019

13. The evolutionary history of dogs in the Americas

Author

Leathlobhair, Máire Ní, 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 J., 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

14. Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

Author

Frantz, Laurent A. F., Rudzinski, Anna, Nugraha, Abang Mansyursyah Surya, Evin, Allowen, Burton, James, Hulme-Beaman, Ardern, Linderholm, Anna, Barnett, Ross, Vega, Rodrigo, Irving-Pease, Evan K., Haile, James, Allen, Richard, Leus, Kristin, Shephard, Jill, Hillyer, Mia, Gillemot, Sarah, van den Hurk, Jeroen, Ogle, Sharron, Atofanei, Cristina, Thomas, Mark G., Johansson, Friederike, Mustari, Abdul Haris, Williams, John, Mohamad, Kusdiantoro, Damayanti, Chandramaya Siska, Wiryadik, Ita Djuwita, Obbles, Dagmar, Mona, Stephano, Day, Hally, Yasin, Muhammad, Meker, Stefan, McGuire, Jimmy A., Evans, Ben J., von Rintelen, Thomas, Ho, Simon Y. W., Searle, Jeremy B., Kitchener, Andrew C., Macdonald, Alastair A., Shaw, Darren J., Hall, Robert, Galbusera, Peter, and Larson, Greger

Published
2018

16. Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland

Author

Linderholm, Anna, Kılınç, Gülşah Merve, Szczepanek, Anita, Włodarczak, Piotr, Jarosz, Paweł, Belka, Zdzislaw, Dopieralska, Jolanta, Werens, Karolina, Górski, Jacek, Mazurek, Mirosław, Hozer, Monika, Rybicka, Małgorzata, Ostrowski, Mikołaj, Bagińska, Jolanta, Koman, Wiesław, Rodríguez-Varela, Ricardo, Storå, Jan, Götherström, Anders, and Krzewińska, Maja

Published
2020
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17. Genomic investigation refutes record of most diverged avian hybrid

Author

Alfieri, James M., Johnson, Taryn, Linderholm, Anna, Blackmon, Heath, Athrey, Giridhar N., Alfieri, James M., Johnson, Taryn, Linderholm, Anna, Blackmon, Heath, and Athrey, Giridhar N.

Abstract

The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the “record” of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.

Published
2023
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18. Genomic and archaeological evidence suggests a dual origin of domestic dogs

Author

Frantz, Laurent A. F., Mullin, Victoria E., Pionnier-Capitan, Maud, Lebrasseur, Ophélie, Ollivier, Morgane, Perri, Angela, Linderholm, Anna, Mattiangeli, Valeria, Teasdale, Matthew D., Dimopoulos, Evangelos A., Tresset, Anne, Duffraisse, Marilyne, McCormick, Finbar, Bartosiewicz, László, Gál, Erika, Nyerge, Éva A., Sablin, Mikhail V., Bréhard, Stéphanie, Mashkour, Marjan, Benjam, Adrian, Gillet, Benjamin, Hughes, Sandrine, Chassaing, Olivier, Hitte, Christophe, Vigne, Jean-Denis, Dobney, Keith, Hänni, Catherine, Bradley, Daniel G., and Larson, Greger

Published
2016

19. The modern freshwater component in Baltic Sea glacial clays

Author

Chen, Nai-Chen, primary, O'Regan, Matthew, additional, Stranne, Christian, additional, Hong, Wei-Li, additional, Roth, Florian, additional, Mörth, Carl-Magnus, additional, Andrén, Thomas, additional, Huang, Tzu-Hao, additional, Regnell, Carl, additional, Linderholm, Anna, additional, Gyllencreutz, Richard, additional, Humborg, Christoph, additional, and Jakobsson, Martin, additional

Published
2023
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22. Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Author

Yu, He [0000-0003-1323-4730], Jamieson, Alexandra [0000-0003-0979-5762], Hulme-Beaman, Ardern [0000-0001-8130-9648], Conroy, Chris J. [0000-0001-7198-9651], Speller, Camilla [0000-0001-7128-9903], Baron, Henriette [0000-0003-4338-3681], Crowther, Alison [0000-0002-2394-1917], Cucchi, Thomas [0000-0001-6021-5001], Fleisher, Jeffrey [0000-0002-6505-9666], Gladilina, Elena [0000-0002-5114-7526], Gol’din, Pavel [0000-0001-6118-1384], Goodman, Steven M. [0000-0001-9318-0570], Kunst, Günther Karl [0000-0002-2175-8641], Linderholm, Anna [0000-0002-1613-9926], Morales-Muñiz, Arturo [0000-0002-9933-6836], Nabais, Mariana [0000-0001-5344-237X], Oueslati, Tarek [0000-0002-2886-085X], Quintana Morales, Eréndira M. [0000-0001-5927-5058], Rannamäe, Eve [0000-0003-1186-5512], Sanmartí Grego, Joan [0000-0002-6635-9249], Valenzuela-Lamas, Silvia [0000-0001-9886-0372], Neer, Wim Van [0000-0003-1710-3623], Vigne, Jean-Denis [0000-0002-7367-7552], Wynne-Jones, Stephanie [0000-0002-3005-8647], Dobney, Keith [0000-0001-9036-4681], Boivin, Nicole [0000-0002-7783-4199], Searle, Jeremy B. [0000-0001-7710-5204], Krause-Kyora, Ben [0000-0001-9435-2872], Krause, Johannes [0000-0001-9144-3920], Larson, Greger [0000-0002-4092-0392], Orton, David [0000-0003-4069-8004], Yu, He, Jamieson, Alexandra, Hulme-Beaman, Ardern, Conroy, Chris J., Knight, Becky, Speller, Camilla, Al-Jarah, Hiba, Eager, Heidi, Trinks, Alexandra, Adikari, Gamini, Baron, Henriette, Böhlendorf-Arslan, Beate, Bohingamuwa, Wijerathne, Crowther, Alison, Cucchi, Thomas, Esser, Kinie, Fleisher, Jeffrey, Gidney, Louisa, Gladilina, Elena, Gol’din, Pavel, Goodman, Steven M., Hamilton-Dyer, Sheila, Helm, Richard, Hillman, Chris, Kallala, Nabil, Kivikero, Hanna, Kovács, Zsófia E., Kunst, Günther Karl, Kyselý, René, Linderholm, Anna, Maraoui-Telmini, Bouthéina, Morales-Muñiz, Arturo, Nabais, Mariana, O’Connor, Terry, Oueslati, Tarek, Quintana Morales, Eréndira M., Pasda, Kerstin, Jude Perera, Perera, Nimal, Radbauer, Silvia, Ramon, Joan, Rannamäe, Eve, Sanmartí Grego, Joan, Treasure, Edward, Valenzuela-Lamas, Silvia, Jagt, Inge van der, Neer, Wim Van, Vigne, Jean-Denis, Walker, Thomas, Wynne-Jones, Stephanie, Zeiler, Jørn, Dobney, Keith, Boivin, Nicole, Searle, Jeremy B., Krause-Kyora, Ben, Krause, Johannes, Larson, Greger, Orton, David, Yu, He [0000-0003-1323-4730], Jamieson, Alexandra [0000-0003-0979-5762], Hulme-Beaman, Ardern [0000-0001-8130-9648], Conroy, Chris J. [0000-0001-7198-9651], Speller, Camilla [0000-0001-7128-9903], Baron, Henriette [0000-0003-4338-3681], Crowther, Alison [0000-0002-2394-1917], Cucchi, Thomas [0000-0001-6021-5001], Fleisher, Jeffrey [0000-0002-6505-9666], Gladilina, Elena [0000-0002-5114-7526], Gol’din, Pavel [0000-0001-6118-1384], Goodman, Steven M. [0000-0001-9318-0570], Kunst, Günther Karl [0000-0002-2175-8641], Linderholm, Anna [0000-0002-1613-9926], Morales-Muñiz, Arturo [0000-0002-9933-6836], Nabais, Mariana [0000-0001-5344-237X], Oueslati, Tarek [0000-0002-2886-085X], Quintana Morales, Eréndira M. [0000-0001-5927-5058], Rannamäe, Eve [0000-0003-1186-5512], Sanmartí Grego, Joan [0000-0002-6635-9249], Valenzuela-Lamas, Silvia [0000-0001-9886-0372], Neer, Wim Van [0000-0003-1710-3623], Vigne, Jean-Denis [0000-0002-7367-7552], Wynne-Jones, Stephanie [0000-0002-3005-8647], Dobney, Keith [0000-0001-9036-4681], Boivin, Nicole [0000-0002-7783-4199], Searle, Jeremy B. [0000-0001-7710-5204], Krause-Kyora, Ben [0000-0001-9435-2872], Krause, Johannes [0000-0001-9144-3920], Larson, Greger [0000-0002-4092-0392], Orton, David [0000-0003-4069-8004], Yu, He, Jamieson, Alexandra, Hulme-Beaman, Ardern, Conroy, Chris J., Knight, Becky, Speller, Camilla, Al-Jarah, Hiba, Eager, Heidi, Trinks, Alexandra, Adikari, Gamini, Baron, Henriette, Böhlendorf-Arslan, Beate, Bohingamuwa, Wijerathne, Crowther, Alison, Cucchi, Thomas, Esser, Kinie, Fleisher, Jeffrey, Gidney, Louisa, Gladilina, Elena, Gol’din, Pavel, Goodman, Steven M., Hamilton-Dyer, Sheila, Helm, Richard, Hillman, Chris, Kallala, Nabil, Kivikero, Hanna, Kovács, Zsófia E., Kunst, Günther Karl, Kyselý, René, Linderholm, Anna, Maraoui-Telmini, Bouthéina, Morales-Muñiz, Arturo, Nabais, Mariana, O’Connor, Terry, Oueslati, Tarek, Quintana Morales, Eréndira M., Pasda, Kerstin, Jude Perera, Perera, Nimal, Radbauer, Silvia, Ramon, Joan, Rannamäe, Eve, Sanmartí Grego, Joan, Treasure, Edward, Valenzuela-Lamas, Silvia, Jagt, Inge van der, Neer, Wim Van, Vigne, Jean-Denis, Walker, Thomas, Wynne-Jones, Stephanie, Zeiler, Jørn, Dobney, Keith, Boivin, Nicole, Searle, Jeremy B., Krause-Kyora, Ben, Krause, Johannes, Larson, Greger, and Orton, David

Abstract

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

Published
2021

26. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast.

Author

vonHoldt, Bridgett M., Brzeski, Kristin E., Aardema, Matthew L., Schell, Christopher J., Rutledge, Linda Y., Fain, Steven R., Shutt, Amy C., Linderholm, Anna, and Murphy, William J.

Subjects
INTROGRESSION (Genetics), WOLVES, REPRODUCTIVE isolation, X chromosome, GENEALOGY, GENE flow
Abstract

Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west‐to‐east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X‐linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf. [ABSTRACT FROM AUTHOR]

Published
2022
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31. Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Author

Yu, He, primary, Jamieson, Alexandra, additional, Hulme-Beaman, Ardern, additional, Conroy, Chris J., additional, Knight, Becky, additional, Speller, Camilla, additional, Al-Jarah, Hiba, additional, Eager, Heidi, additional, Trinks, Alexandra, additional, Adikari, Gamini, additional, Baron, Henriette, additional, Böhlendorf-Arslan, Beate, additional, Bohingamuwa, Wijerathne, additional, Crowther, Alison, additional, Cucchi, Thomas, additional, Esser, Kinie, additional, Fleisher, Jeffrey, additional, Gidney, Louisa, additional, Gladilina, Elena, additional, Gol’din, Pavel, additional, Goodman, Steven M., additional, Hamilton-Dyer, Sheila, additional, Helm, Richard, additional, Hillman, Chris, additional, Kallala, Nabil, additional, Kivikero, Hanna, additional, Kovács, Zsófia E., additional, Karl Kunst, Günther, additional, Kyselý, René, additional, Linderholm, Anna, additional, Maraoui-Telmini, Bouthéina, additional, Morales-Muñiz, Arturo, additional, Nabais, Mariana, additional, O’Connor, Terry, additional, Oueslati, Tarek, additional, Quintana Morales, Eréndira M., additional, Pasda, Kerstin, additional, Perera, Jude, additional, Perera, Nimal, additional, Radbauer, Silvia, additional, Ramon, Joan, additional, Rannamäe, Eve, additional, Sanmartí Grego, Joan, additional, Treasure, Edward, additional, Valenzuela-Lamas, Silvia, additional, van der Jagt, Inge, additional, Van Neer, Wim, additional, Vigne, Jean-Denis, additional, Walker, Thomas, additional, Wynne-Jones, Stephanie, additional, Zeiler, Jørn, additional, Dobney, Keith, additional, Boivin, Nicole, additional, Searle, Jeremy B., additional, Krause-Kyora, Ben, additional, Krause, Johannes, additional, Larson, Greger, additional, and Orton, David, additional

Published
2021
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32. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Battista Vincent M,Linderholm Anna,Mullin Victoria E,Daly Kevin G,Price Max,Gron Kurt J,Alexandri Panoraia,Arbogast Rose-Marie,Arbuckle Benjamin,Adrian B?l?şescu,Barnett Ross,Bartosiewicz László,Baryshnikov Gennady,Bonsall Clive,Laurent A F Frantz,Boric Dušan,Boroneant Adina,Jelena Bulatovic,Çakirlar Canan,Carretero José-Miguel,Chapman John,Church Mike,Crooijmans Richard,De Cupere Bea,Dimitrijevic Vesna,Laurent A F Frantz,Detry Cleia,Dumitraşcu Valentin,du Plessis Louis,Haile James,Audrey T Lin,Amelia Scheu,Christina Görg,Benecke Norbert,Ceiridwen J Edwards,EREK CEVDET MERİH,Alexander Michelle

Subjects
Arkeoloji
Published
2020

33. Complete Supplementary Documents from A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids

Author

Allen, Richard, Ryan, Hannah, Davis, Brian W., King, Charlotte, Frantz, Laurent, Irving-Pease, Evan, Barnett, Ross, Linderholm, Anna, Loog, Liisa, Haile, James, Lebrasseur, Ophélie, White, Mark, Kitchener, Andrew C., Murphy, William J., and Larson, Greger

Abstract

Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F1 hybrids are able to produce F2 s through matings with F1 s. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species due to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid offspring can produce F2 s. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.

Published
2020
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34. Erratum: Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A.F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose Marie, Arbuckle, Benjamin, Bǎlǎşescu, Adrian, Barnettl, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, Jose Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoǧan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jorg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, Francois Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Van Den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Subjects
Aquaculture and Fisheries, Aquacultuur en Visserij, WIAS, Life Science, Fokkerij en Genomica, Animal Breeding and Genomics
Abstract

The authors note that the affiliation for Alexandros Triantafyllidis and Panoraia Alexandri should be listed as Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; and that the affiliation for Rose-Marie Arbogast should be listed as CNRS UMR 7044, Maison interuniversitaire des sciences de l'Homme, F-67083 Strasbourg Cedex, France. The corrected author and affiliation lines appear below. The online version has been corrected.

Published
2020

35. Viking Mobility in the Baltic Sea Region

Author

Hedenstierna-Jonson, Charlotte, Linderholm, Anna, Kjellström, Anna, Hedenstierna-Jonson, Charlotte, Linderholm, Anna, and Kjellström, Anna

Abstract

Tough mobility and migration could be regarded as diagnostic features of the Viking Age, it is not possible to generalize and treat the Viking World as a homogenous society. Patterns of mobility and migration were linked to social structures and contexts. Studying the composition of the material culture within a site or individual context has been the prevailing method within archaeology to approach issues of mobility. Although this approach has acknowledged restrictions, it has been the method at hand. However, migration and mobility are not necessarily reflected in the material culture, meaning other approaches are called for. The first question to ask is: what variations in mobility patterns between urban and rural contexts are there, and are there indications of significant differences between various geographical regions? Even between sites characterized as trading posts (i.e. not rural), with similar material evidence of long-distance trade and advanced crafts, we might have significant differences, relating to the seasonal or permanent character of the site. In the following paper, we present the results from strontium isotope analyses on archaeological materials from a number of Viking-Age sites within present-day Sweden. The results of the analyses conducted within the ATLAS project will be compared to other isotope studies from Scandinavia, and discussed in relation to local, regional and supra-regional contexts. On a more local level, the possible cultural influence of migrants is investigated.

Published
2020

36. Origins and genetic legacy of prehistoric dogs

Author

Bergström, Anders, Frantz, Laurent, Schmidt, Ryan, Ersmark, Erik, Lebrasseur, Ophelie, Girdland-Flink, Linus, Lin, Audrey T., Storå, Jan, Sjögren, Karl-Göran, Anthony, David, Antipina, Ekaterina, Amiri, Sarieh, Bar-Oz, Guy, Bazaliiskii, Vladimir I., Bulatovic, Jelena, Brown, Dorcas, Carmagnini, Alberto, Davy, Tom, Fedorov, Sergey, Fiore, Ivana, Fulton, Deirdre, Germonpré, Mietje, Haile, James, Irving-Pease, Evan K., Jamieson, Alexandra, Janssens, Luc, Kirillova, Irina, Horwitz, Liora Kolska, Kuzmanovic-Cvetkovic, Julka, Kuzmin, Yaroslav, Losey, Robert J., Ložnjak Dizdar, Daria, Mashkour, Marjan, Novak, Mario, Onar, Vedat, Orton, David, Pasaric, Maja, Radivojevic, Miljana, Rajkovic, Dragana, Roberts, Benjamin, Ryan, Hannah, Sablin, Mikhail, Shidlovskiy, Fedor, Stojanovic, Ivana, Tagliacozzo, Antonio, Trantalidou, Katerina, Ullén, Inga, Villaluenga, Aritza, Wapnish, Paula, Dobney, Keith, Götherström, Anders, Linderholm, Anna, Dalén, Love, Pinhasi, Ron, Larson, Greger, Skoglund, Pontus, Bergström, Anders, Frantz, Laurent, Schmidt, Ryan, Ersmark, Erik, Lebrasseur, Ophelie, Girdland-Flink, Linus, Lin, Audrey T., Storå, Jan, Sjögren, Karl-Göran, Anthony, David, Antipina, Ekaterina, Amiri, Sarieh, Bar-Oz, Guy, Bazaliiskii, Vladimir I., Bulatovic, Jelena, Brown, Dorcas, Carmagnini, Alberto, Davy, Tom, Fedorov, Sergey, Fiore, Ivana, Fulton, Deirdre, Germonpré, Mietje, Haile, James, Irving-Pease, Evan K., Jamieson, Alexandra, Janssens, Luc, Kirillova, Irina, Horwitz, Liora Kolska, Kuzmanovic-Cvetkovic, Julka, Kuzmin, Yaroslav, Losey, Robert J., Ložnjak Dizdar, Daria, Mashkour, Marjan, Novak, Mario, Onar, Vedat, Orton, David, Pasaric, Maja, Radivojevic, Miljana, Rajkovic, Dragana, Roberts, Benjamin, Ryan, Hannah, Sablin, Mikhail, Shidlovskiy, Fedor, Stojanovic, Ivana, Tagliacozzo, Antonio, Trantalidou, Katerina, Ullén, Inga, Villaluenga, Aritza, Wapnish, Paula, Dobney, Keith, Götherström, Anders, Linderholm, Anna, Dalén, Love, Pinhasi, Ron, Larson, Greger, and Skoglund, Pontus

Abstract

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

Published
2020
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37. 'Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe (vol 116, pg17231, 2019)

Author

Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneant, Adina, Bulatović, Jelena, Cakirlar, Canan, Carreterow, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijević, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Ash, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jorg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, Larson, Greger, Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geoerg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balasescu, Adrian, Barnett, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneant, Adina, Bulatović, Jelena, Cakirlar, Canan, Carreterow, Jose-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijević, Vesna, Dumitrascu, Valentin, du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Ozdogan, Ash, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Gotherstrom, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Josephine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jorg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, Francois-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2020

38. Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change

Author

Seersholm, Frederik V., Werndly, Daniel J., Grealy, Alicia, Johnson, Taryn, Keenan Early, Erin M., Lundelius, Ernest L., Winsborough, Barbara, Farr, Grayal Earle, Toomey, Rickard, Hansen, Anders J., Shapiro, Beth, Waters, Michael R., McDonald, Gregory, Linderholm, Anna, Stafford, Thomas W., Bunce, Michael, Seersholm, Frederik V., Werndly, Daniel J., Grealy, Alicia, Johnson, Taryn, Keenan Early, Erin M., Lundelius, Ernest L., Winsborough, Barbara, Farr, Grayal Earle, Toomey, Rickard, Hansen, Anders J., Shapiro, Beth, Waters, Michael R., McDonald, Gregory, Linderholm, Anna, Stafford, Thomas W., and Bunce, Michael

Abstract

Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall’s Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.

Published
2020

39. Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics

Author

Ottoni, Claudio, Girdland Flink, Linus, Evin, Allowen, Geörg, Christina, De Cupere, Bea, Van Neer, Wim, Bartosiewicz, László, Linderholm, Anna, Barnett, Ross, Peters, Joris, Decorte, Ronny, Waelkens, Marc, Vanderheyden, Nancy, Ricaut, François-Xavier, Çakrlar, Canan, Çevik, Özlem, Hoelzel, A. Rus, Mashkour, Marjan, Mohaseb Karimlu, Azadeh Fatemeh, Sheikhi Seno, Shiva, Daujat, Julie, Brock, Fiona, Pinhasi, Ron, Hongo, Hitomi, Perez-Enciso, Miguel, Rasmussen, Morten, Frantz, Laurent, Megens, Hendrik-Jan, Crooijmans, Richard, Groenen, Martien, Arbuckle, Benjamin, Benecke, Nobert, Strand Vidarsdottir, Una, Burger, Joachim, Cucchi, Thomas, Dobney, Keith, and Larson, Greger

Published
2013
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41. Who We Are and How We Got Here

Author

Linderholm, Anna, Horsburgh, K. Ann, Vander Linden, Marc, Klein, Richard G., Bandelt, Hans-Jürgen, and Kirch, Patrick V.

Published
2018

42. Origins and genetic legacy of prehistoric dogs

Author

Bergström, Anders, primary, Frantz, Laurent, additional, Schmidt, Ryan, additional, Ersmark, Erik, additional, Lebrasseur, Ophelie, additional, Girdland-Flink, Linus, additional, Lin, Audrey T., additional, Storå, Jan, additional, Sjögren, Karl-Göran, additional, Anthony, David, additional, Antipina, Ekaterina, additional, Amiri, Sarieh, additional, Bar-Oz, Guy, additional, Bazaliiskii, Vladimir I., additional, Bulatović, Jelena, additional, Brown, Dorcas, additional, Carmagnini, Alberto, additional, Davy, Tom, additional, Fedorov, Sergey, additional, Fiore, Ivana, additional, Fulton, Deirdre, additional, Germonpré, Mietje, additional, Haile, James, additional, Irving-Pease, Evan K., additional, Jamieson, Alexandra, additional, Janssens, Luc, additional, Kirillova, Irina, additional, Horwitz, Liora Kolska, additional, Kuzmanovic-Cvetković, Julka, additional, Kuzmin, Yaroslav, additional, Losey, Robert J., additional, Dizdar, Daria Ložnjak, additional, Mashkour, Marjan, additional, Novak, Mario, additional, Onar, Vedat, additional, Orton, David, additional, Pasarić, Maja, additional, Radivojević, Miljana, additional, Rajković, Dragana, additional, Roberts, Benjamin, additional, Ryan, Hannah, additional, Sablin, Mikhail, additional, Shidlovskiy, Fedor, additional, Stojanović, Ivana, additional, Tagliacozzo, Antonio, additional, Trantalidou, Katerina, additional, Ullén, Inga, additional, Villaluenga, Aritza, additional, Wapnish, Paula, additional, Dobney, Keith, additional, Götherström, Anders, additional, Linderholm, Anna, additional, Dalén, Love, additional, Pinhasi, Ron, additional, Larson, Greger, additional, and Skoglund, Pontus, additional

Published
2020
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44. Bioarchaeological field analysis of human remains from the mass graves at Phaleron, Greece. With an introduction by Stella Chryssoulaki and an appendix by Anna Linderholm, Anna Kjellström, Vendela Kempe Lagerholm, & Maja Krzewińska

Author

Ingvarsson, Anne, primary, Bäckström, Ylva, additional, Chryssoulaki, Stella, additional, Linderholm, Anna, additional, Kjellström, Anna, additional, Kempe Lagerholm, Vendela, additional, and Krzewińska, Maja, additional

Published
2019
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45. Supplementary text from Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author

Ameen, Carly, Feuerborn, Tatiana R., Brown, Sarah K., Linderholm, Anna, Ardern Hulme-Beaman, Lebrasseur, Ophélie, Mikkel-Holger S. Sinding, Lounsberry, Zachary T., Lin, Audrey T., Appelt, Martin, Bachmann, Lutz, Betts, Matthew, Britton, Kate, Darwent, John, Dietz, Rune, Fredholm, Merete, Gopalakrishnan, Shyam, Goriunova, Olga I., Grønnow, Bjarne, Haile, James, Hallsson, Jón Hallsteinn, Harrison, Ramona, Heide-Jørgensen, Mads Peter, Knecht, Rick, Losey, Robert J., Masson-MacLean, Edouard, McGovern, Thomas H., McManus-Fry, Ellen, Meldgaard, Morten, Midtdal, Åslaug, Moss, Madonna L., Nikitin, Iurii G., Nomokonova, Tatiana, Pálsdóttir, Albína Hulda, Perri, Angela, Popov, Aleksandr N., Rankin, Lisa, Reuther, Joshua D., Sablin, Mikhail, Schmidt, Anne Lisbeth, Shirar, Scott, Smiarowski, Konrad, Sonne, Christian, Stiner, Mary C., Mitya Vasyukov, West, Catherine F., Ween, Gro Birgit, Wennerberg, Sanne Eline, Wiig, Øystein, Woollett, James, Dalén, Love, Hansen, Anders J., Gilbert, Tom, Sacks, Benjamin, Frantz, Laurent, Larson, Greger, Dobney, Keith, Christyann M. Darwent, and Allowen Evin

Subjects
geographic locations
Abstract

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Published
2019
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46. Supplementary captions for Figures S1 - S17 and captions for Databases S1 to S6 from Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author

Ameen, Carly, Feuerborn, Tatiana R., Brown, Sarah K., Linderholm, Anna, Ardern Hulme-Beaman, Lebrasseur, Ophélie, Mikkel-Holger S. Sinding, Lounsberry, Zachary T., Lin, Audrey T., Appelt, Martin, Bachmann, Lutz, Betts, Matthew, Britton, Kate, Darwent, John, Dietz, Rune, Fredholm, Merete, Gopalakrishnan, Shyam, Goriunova, Olga I., Grønnow, Bjarne, Haile, James, Hallsson, Jón Hallsteinn, Harrison, Ramona, Heide-Jørgensen, Mads Peter, Knecht, Rick, Losey, Robert J., Masson-MacLean, Edouard, McGovern, Thomas H., McManus-Fry, Ellen, Meldgaard, Morten, Midtdal, Åslaug, Moss, Madonna L., Nikitin, Iurii G., Nomokonova, Tatiana, Pálsdóttir, Albína Hulda, Perri, Angela, Popov, Aleksandr N., Rankin, Lisa, Reuther, Joshua D., Sablin, Mikhail, Schmidt, Anne Lisbeth, Shirar, Scott, Smiarowski, Konrad, Sonne, Christian, Stiner, Mary C., Mitya Vasyukov, West, Catherine F., Ween, Gro Birgit, Wennerberg, Sanne Eline, Wiig, Øystein, Woollett, James, Dalén, Love, Hansen, Anders J., Gilbert, Tom, Sacks, Benjamin, Frantz, Laurent, Larson, Greger, Dobney, Keith, Christyann M. Darwent, and Allowen Evin

Subjects
geographic locations
Abstract

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Published
2019
Full Text
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47. Figs. S1 to S17 from Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author

Ameen, Carly, Feuerborn, Tatiana R., Brown, Sarah K., Linderholm, Anna, Ardern Hulme-Beaman, Lebrasseur, Ophélie, Mikkel-Holger S. Sinding, Lounsberry, Zachary T., Lin, Audrey T., Appelt, Martin, Bachmann, Lutz, Betts, Matthew, Britton, Kate, Darwent, John, Dietz, Rune, Fredholm, Merete, Gopalakrishnan, Shyam, Goriunova, Olga I., Grønnow, Bjarne, Haile, James, Hallsson, Jón Hallsteinn, Harrison, Ramona, Heide-Jørgensen, Mads Peter, Knecht, Rick, Losey, Robert J., Masson-MacLean, Edouard, McGovern, Thomas H., McManus-Fry, Ellen, Meldgaard, Morten, Midtdal, Åslaug, Moss, Madonna L., Nikitin, Iurii G., Nomokonova, Tatiana, Pálsdóttir, Albína Hulda, Perri, Angela, Popov, Aleksandr N., Rankin, Lisa, Reuther, Joshua D., Sablin, Mikhail, Schmidt, Anne Lisbeth, Shirar, Scott, Smiarowski, Konrad, Sonne, Christian, Stiner, Mary C., Mitya Vasyukov, West, Catherine F., Ween, Gro Birgit, Wennerberg, Sanne Eline, Wiig, Øystein, Woollett, James, Dalén, Love, Hansen, Anders J., Gilbert, Tom, Sacks, Benjamin, Frantz, Laurent, Larson, Greger, Dobney, Keith, Christyann M. Darwent, and Allowen Evin

Subjects
geographic locations
Abstract

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Paleo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Paleo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Paleo-Inuit dogs, and most likely aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Published
2019
Full Text
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48. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Piperno, Dolores R., Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Bălăşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakırlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, DeCupere, Bea, Detry, Cleia, Dimitrijević, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen, Erek, Cevdet Merih, Erim Özdoğan, Aslı, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora Kolska, Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaserya, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Motuzaitė Matuzevičiūtė, Giedrė, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Parker Pearson, Michael, Pinhasi, Ron, Radmanović, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad N., Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Hurk, Youri van den, Poucke, Sophie van, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, Larson, Greger, Piperno, Dolores R., Frantz, Laurent A. F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Bălăşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakırlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, DeCupere, Bea, Detry, Cleia, Dimitrijević, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen, Erek, Cevdet Merih, Erim Özdoğan, Aslı, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora Kolska, Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaserya, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Motuzaitė Matuzevičiūtė, Giedrė, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Parker Pearson, Michael, Pinhasi, Ron, Radmanović, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad N., Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Hurk, Youri van den, Poucke, Sophie van, Vigne, Jean-Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Abstract

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Published
2019

49. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A.F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose Marie, Arbuckle, Benjamin, Bǎlǎşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, José Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoǧan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, François Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Van Den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M.T.P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, Larson, Greger, Frantz, Laurent A.F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose Marie, Arbuckle, Benjamin, Bǎlǎşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, José Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoǧan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, François Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Van Den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, M.T.P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Abstract

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Published
2019

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