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533 results on '"Sinding, Mikkel-holger S"'

1. The genomic natural history of the aurochs

Author

Rossi, Conor, Sinding, Mikkel-Holger S., Mullin, Victoria E., Scheu, Amelie, Erven, Jolijn A. M., Verdugo, Marta Pereira, Daly, Kevin G., Ciucani, Marta Maria, Mattiangeli, Valeria, Teasdale, Matthew D., Diquelou, Deborah, Manin, Aurélie, Bangsgaard, Pernille, Collins, Matthew, Lord, Tom C., Zeibert, Viktor, Zorzin, Roberto, Vinter, Michael, Timmons, Zena, Kitchener, Andrew C., Street, Martin, Haruda, Ashleigh F., Tabbada, Kristina, Larson, Greger, Frantz, Laurent A. F., Gehlen, Birgit, Alhaique, Francesca, Tagliacozzo, Antonio, Fornasiero, Mariagabriella, Pandolfi, Luca, Karastoyanova, Nadezhda, Sørensen, Lasse, Kiryushin, Kirill, Ekström, Jonas, Mostadius, Maria, Grandal-d’Anglade, Aurora, Vidal-Gorosquieta, Amalia, Benecke, Norbert, Kropp, Claus, Grushin, Sergei P., Gilbert, M. Thomas P., Merts, Ilja, Merts, Viktor, Outram, Alan K., Rosengren, Erika, Kosintsev, Pavel, Sablin, Mikhail, Tishkin, Alexey A., Makarewicz, Cheryl A., Burger, Joachim, and Bradley, Daniel G.

Published
2024
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2. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations

Author

Liu, Xiaodong, Lin, Long, Sinding, Mikkel-Holger S., Bertola, Laura D., Hanghøj, Kristian, Quinn, Liam, Garcia-Erill, Genís, Rasmussen, Malthe Sebro, Schubert, Mikkel, Pečnerová, Patrícia, Balboa, Renzo F., Li, Zilong, Heaton, Michael P., Smith, Timothy P. L., Pinto, Rui Resende, Wang, Xi, Kuja, Josiah, Brüniche-Olsen, Anna, Meisner, Jonas, Santander, Cindy G., Ogutu, Joseph O., Masembe, Charles, da Fonseca, Rute R., Muwanika, Vincent, Siegismund, Hans R., Albrechtsen, Anders, Moltke, Ida, and Heller, Rasmus

Published
2024
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4. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Author

Balboa, Renzo F., Bertola, Laura D., Brüniche-Olsen, Anna, Rasmussen, Malthe Sebro, Liu, Xiaodong, Besnard, Guillaume, Salmona, Jordi, Santander, Cindy G., He, Shixu, Zinner, Dietmar, Pedrono, Miguel, Muwanika, Vincent, Masembe, Charles, Schubert, Mikkel, Kuja, Josiah, Quinn, Liam, Garcia-Erill, Genís, Stæger, Frederik Filip, Rakotoarivony, Rianja, Henrique, Margarida, Lin, Long, Wang, Xi, Heaton, Michael P., Smith, Timothy P. L., Hanghøj, Kristian, Sinding, Mikkel-Holger S., Atickem, Anagaw, Chikhi, Lounès, Roos, Christian, Gaubert, Philippe, Siegismund, Hans R., Moltke, Ida, Albrechtsen, Anders, and Heller, Rasmus

Published
2024
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5. Evolution and legacy of East Asian aurochs

Author

Hou, Jiawen, Guan, Xiwen, Xia, Xiaoting, Lyu, Yang, Liu, Xin, Mazei, Yuri, Xie, Ping, Chang, Fengqin, Zhang, Xiaonan, Chen, Jialei, Li, Xinyi, Zhang, Fengwei, Jin, Liangliang, Luo, Xiaoyu, Sinding, Mikkel-Holger S., Sun, Xin, Achilli, Alessandro, Migliore, Nicola Rambaldi, Zhang, Dongju, Lenstra, Johannes A., Han, Jianlin, Fu, Qiaomei, Liu, Xinyi, Zhang, Xiaoming, Chen, Ningbo, Lei, Chuzhao, and Zhang, Hucai

Published
2024
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7. 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

8. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Author

Chen, Ningbo, Xia, Xiaoting, Hanif, Quratulain, Zhang, Fengwei, Dang, Ruihua, Huang, Bizhi, Lyu, Yang, Luo, Xiaoyu, Zhang, Hucai, Yan, Huixuan, Wang, Shikang, Wang, Fuwen, Chen, Jialei, Guan, Xiwen, Liu, Yangkai, Li, Shuang, Jin, Liangliang, Wang, Pengfei, Sun, Luyang, Zhang, Jicai, Liu, Jianyong, Qu, Kaixing, Cao, Yanhong, Sun, Junli, Liao, Yuying, Xiao, Zhengzhong, Cai, Ming, Mu, Lan, Siddiki, Amam Zonaed, Asif, Muhammad, Mansoor, Shahid, Babar, Masroor Ellahi, Hussain, Tanveer, Silva, Gamamada Liyanage Lalanie Pradeepa, Gorkhali, Neena Amatya, Terefe, Endashaw, Belay, Gurja, Tijjani, Abdulfatai, Zegeye, Tsadkan, Gebre, Mebrate Genet, Ma, Yun, Wang, Yu, Huang, Yongzhen, Lan, Xianyong, Chen, Hong, Migliore, Nicola Rambaldi, Colombo, Giulia, Semino, Ornella, Achilli, Alessandro, Sinding, Mikkel-Holger S., Lenstra, Johannes A., Cheng, Haijian, Lu, Wenfa, Hanotte, Olivier, Han, Jianlin, Jiang, Yu, and Lei, Chuzhao

Published
2023
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9. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Author

Louis, Marie, Korlević, Petra, Nykänen, Milaja, Archer, Frederick, Berrow, Simon, Brownlow, Andrew, Lorenzen, Eline D., O’Brien, Joanne, Post, Klaas, Racimo, Fernando, Rogan, Emer, Rosel, Patricia E., Sinding, Mikkel-Holger S., van der Es, Henry, Wales, Nathan, Fontaine, Michael C., Gaggiotti, Oscar E., and Foote, Andrew D.

Published
2023
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11. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
General Science & Technology
Abstract

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Published
2021

12. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

Author

Ciucani, Marta Maria, Ramos-Madrigal, Jazmín, Hernández-Alonso, Germán, Carmagnini, Alberto, Aninta, Sabhrina Gita, Sun, Xin, Scharff-Olsen, Camilla Hjorth, Lanigan, Liam Thomas, Fracasso, Ilaria, Clausen, Cecilie G., Aspi, Jouni, Kojola, Ilpo, Baltrūnaitė, Laima, Balčiauskas, Linas, Moore, Jane, Åkesson, Mikael, Saarma, Urmas, Hindrikson, Maris, Hulva, Pavel, Bolfíková, Barbora Černá, Nowak, Carsten, Godinho, Raquel, Smith, Steve, Paule, Ladislav, Nowak, Sabina, Mysłajek, Robert W., Lo Brutto, Sabrina, Ciucci, Paolo, Boitani, Luigi, Vernesi, Cristiano, Stenøien, Hans K., Smith, Oliver, Frantz, Laurent, Rossi, Lorenzo, Angelici, Francesco Maria, Cilli, Elisabetta, Sinding, Mikkel-Holger S., Gilbert, M. Thomas P., and Gopalakrishnan, Shyam

Published
2023
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13. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Life on Land, Animals, Birds, Chickens, Conservation of Natural Resources, Datasets as Topic, Finches, Genome, Genomics, Humans, Phylogeny, Selection, Genetic, Synteny, General Science & Technology
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

14. 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

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

Author

Feuerborn, Tatiana R., Carmagnini, Alberto, Losey, Robert J., Nomokonova, Tatiana, Askeyev, Arthur, Askeyev, Igor, Askeyev, Oleg, Antipina, Ekaterina E., Appelt, Martin, Bachura, Olga P., Beglane, Fiona, Bradley, Daniel G., Daly, Kevin G., Gopalakrishnan, Shyam, Gregersen, Kristian Murphy, Guo, Chunxue, Gusev, Andrei V., Jones, Carleton, Kosintsev, Pavel A., Kuzmin, Yaroslav V., Mattiangeli, Valeria, Perri, Angela R., Plekhanov, Andrei V., Ramos-Madrigal, Jazmín, Schmidt, Anne Lisbeth, Shaymuratova, Dilyara, Smith, Oliver, Yavorskaya, Lilia V., Zhang, Guojie, Willerslev, Eske, Meldgaard, Morten, Gilbert, M. Thomas P., Larson, Greger, Dalén, Love, Hansen, Anders J., Sinding, Mikkel-Holger S., and Frantz, Laurent

Published
2021

16. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.

Author

Thomas, Jessica E, Carvalho, Gary R, Haile, James, Rawlence, Nicolas J, Martin, Michael D, Ho, Simon Yw, Sigfússon, Arnór Þ, Jósefsson, Vigfús A, Frederiksen, Morten, Linnebjerg, Jannie F, Samaniego Castruita, Jose A, Niemann, Jonas, Sinding, Mikkel-Holger S, Sandoval-Velasco, Marcela, Soares, André Er, Lacy, Robert, Barilaro, Christina, Best, Juila, Brandis, Dirk, Cavallo, Chiara, Elorza, Mikelo, Garrett, Kimball L, Groot, Maaike, Johansson, Friederike, Lifjeld, Jan T, Nilson, Göran, Serjeanston, Dale, Sweet, Paul, Fuller, Errol, Hufthammer, Anne Karin, Meldgaard, Morten, Fjeldså, Jon, Shapiro, Beth, Hofreiter, Michael, Stewart, John R, Gilbert, M Thomas P, and Knapp, Michael

Subjects
Animals, Humans, DNA, Mitochondrial, Population Dynamics, Phylogeny, Charadriiformes, Extinction, Biological, Genome, Mitochondrial, Genetic Variation, DNA, Ancient, 19th century extinction, ancient DNA, evolutionary biology, genetics, genomics, hunting, paleogenetics, seabird exploitation, Life on Land, Biochemistry and Cell Biology
Abstract

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

Published
2019

17. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Author

Cappellini, Enrico, Welker, Frido, Pandolfi, Luca, Ramos-Madrigal, Jazmín, Samodova, Diana, Rüther, Patrick L, Fotakis, Anna K, Lyon, David, Moreno-Mayar, J Víctor, Bukhsianidze, Maia, Rakownikow Jersie-Christensen, Rosa, Mackie, Meaghan, Ginolhac, Aurélien, Ferring, Reid, Tappen, Martha, Palkopoulou, Eleftheria, Dickinson, Marc R, Stafford, Thomas W, Chan, Yvonne L, Götherström, Anders, Nathan, Senthilvel KSS, Heintzman, Peter D, Kapp, Joshua D, Kirillova, Irina, Moodley, Yoshan, Agusti, Jordi, Kahlke, Ralf-Dietrich, Kiladze, Gocha, Martínez-Navarro, Bienvenido, Liu, Shanlin, Sandoval Velasco, Marcela, Sinding, Mikkel-Holger S, Kelstrup, Christian D, Allentoft, Morten E, Orlando, Ludovic, Penkman, Kirsty, Shapiro, Beth, Rook, Lorenzo, Dalén, Love, Gilbert, M Thomas P, Olsen, Jesper V, Lordkipanidze, David, and Willerslev, Eske

Subjects
Biotechnology, Genetics, Amino Acid Motifs, Amino Acid Sequence, Animals, Bayes Theorem, DNA, Ancient, Dental Enamel, Fossils, History, Ancient, Humans, Male, Perissodactyla, Phosphorylation, Phylogeny, Proteome, Proteomics, General Science & Technology
Abstract

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

Published
2019

19. Genomic insights into the secondary aquatic transition of penguins

Author

Cole, Theresa L., Zhou, Chengran, Fang, Miaoquan, Pan, Hailin, Ksepka, Daniel T., Fiddaman, Steven R., Emerling, Christopher A., Thomas, Daniel B., Bi, Xupeng, Fang, Qi, Ellegaard, Martin R., Feng, Shaohong, Smith, Adrian L., Heath, Tracy A., Tennyson, Alan J. D., Borboroglu, Pablo García, Wood, Jamie R., Hadden, Peter W., Grosser, Stefanie, Bost, Charles-André, Cherel, Yves, Mattern, Thomas, Hart, Tom, Sinding, Mikkel-Holger S., Shepherd, Lara D., Phillips, Richard A., Quillfeldt, Petra, Masello, Juan F., Bouzat, Juan L., Ryan, Peter G., Thompson, David R., Ellenberg, Ursula, Dann, Peter, Miller, Gary, Dee Boersma, P., Zhao, Ruoping, Gilbert, M. Thomas P., Yang, Huanming, Zhang, De-Xing, and Zhang, Guojie

Published
2022
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20. Giraffe lineages are shaped by major ancient admixture events

Author

Bertola, Laura D., primary, Quinn, Liam, additional, Hanghøj, Kristian, additional, Garcia-Erill, Genís, additional, Rasmussen, Malthe Sebro, additional, Balboa, Renzo F., additional, Meisner, Jonas, additional, Bøggild, Thomas, additional, Wang, Xi, additional, Lin, Long, additional, Nursyifa, Casia, additional, Liu, Xiaodong, additional, Li, Zilong, additional, Chege, Mumbi, additional, Moodley, Yoshan, additional, Brüniche-Olsen, Anna, additional, Kuja, Josiah, additional, Schubert, Mikkel, additional, Agaba, Morris, additional, Santander, Cindy G., additional, Sinding, Mikkel-Holger S., additional, Muwanika, Vincent, additional, Masembe, Charles, additional, Siegismund, Hans R., additional, Moltke, Ida, additional, Albrechtsen, Anders, additional, and Heller, Rasmus, additional

Published
2024
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23. Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos

Author

Sinding, Mikkel-Holger S., Ciucani, Marta M., Ramos-Madrigal, Jazmín, Carmagnini, Alberto, Rasmussen, Jacob Agerbo, Feng, Shaohong, Chen, Guangji, Vieira, Filipe G., Mattiangeli, Valeria, Ganjoo, Rajinder K., Larson, Greger, Sicheritz-Pontén, Thomas, Petersen, Bent, Frantz, Laurent, Gilbert, M. Thomas P., and Bradley, Daniel G.

Published
2021
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24. The evolutionary history of extinct and living lions

Author

de Manuel, Marc, Barnett, Ross, Sandoval-Velasco, Marcela, Yamaguchi, Nobuyuki, Vieira, Filipe Garrett, Mendoza, M. Lisandra Zepeda, Liu, Shiping, Martin, Michael D., Sinding, Mikkel-Holger S., Mak, Sarah S. T., Carøe, Christian, Liu, Shanlin, Guo, Chunxue, Zheng, Jiao, Zazula, Grant, Baryshnikov, Gennady, Eizirik, Eduardo, Koepfli, Klaus-Peter, Johnson, Warren E., Antunes, Agostinho, Sicheritz-Ponten, Thomas, Gopalakrishnan, Shyam, Larson, Greger, Yang, Huanming, O’Brien, Stephen J., Hansen, Anders J., Zhang, Guojie, Marques-Bonet, Tomas, and Gilbert, M. Thomas P.

Published
2020

26. Population genomics of the muskox' resilience in the near absence of genetic variation

Author

Pečnerová, Patrícia, Lord, Edana, Garcia-Erill, Genís, Hanghøj, Kristian, Rasmussen, Malthe Sebro, Meisner, Jonas, Liu, Xiaodong, van der Valk, Tom, Santander, Cindy G., Quinn, Liam, Lin, Long, Liu, Shanlin, Carøe, Christian, Dalerum, Fredrik, Götherström, Anders, Måsviken, Johannes, Vartanyan, Sergey, Raundrup, Katrine, Al-Chaer, Amal, Rasmussen, Linett, Hvilsom, Christina, Heide-Jørgensen, Mads Peter, Sinding, Mikkel-Holger S., Aastrup, Peter, Van Coeverden de Groot, Peter J., Schmidt, Niels Martin, Albrechtsen, Anders, Dalén, Love, Heller, Rasmus, Moltke, Ida, Redlef Siegismund, Hans, Pečnerová, Patrícia, Lord, Edana, Garcia-Erill, Genís, Hanghøj, Kristian, Rasmussen, Malthe Sebro, Meisner, Jonas, Liu, Xiaodong, van der Valk, Tom, Santander, Cindy G., Quinn, Liam, Lin, Long, Liu, Shanlin, Carøe, Christian, Dalerum, Fredrik, Götherström, Anders, Måsviken, Johannes, Vartanyan, Sergey, Raundrup, Katrine, Al-Chaer, Amal, Rasmussen, Linett, Hvilsom, Christina, Heide-Jørgensen, Mads Peter, Sinding, Mikkel-Holger S., Aastrup, Peter, Van Coeverden de Groot, Peter J., Schmidt, Niels Martin, Albrechtsen, Anders, Dalén, Love, Heller, Rasmus, Moltke, Ida, and Redlef Siegismund, Hans

Abstract

Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.

Published
2024
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27. Giraffe lineages are shaped by major ancient admixture events

Author

Bertola, Laura D., Quinn, Liam, Hanghøj, Kristian, Garcia-Erill, Genís, Rasmussen, Malthe Sebro, Balboa, Renzo F., Meisner, Jonas, Bøggild, Thomas, Wang, Xi, Lin, Long, Nursyifa, Casia, Liu, Xiaodong, Li, Zilong, Chege, Mumbi, Moodley, Yoshan, Brüniche-Olsen, Anna, Kuja, Josiah, Schubert, Mikkel, Agaba, Morris, Santander, Cindy G., Sinding, Mikkel Holger S., Muwanika, Vincent, Masembe, Charles, Siegismund, Hans R., Moltke, Ida, Albrechtsen, Anders, Heller, Rasmus, Bertola, Laura D., Quinn, Liam, Hanghøj, Kristian, Garcia-Erill, Genís, Rasmussen, Malthe Sebro, Balboa, Renzo F., Meisner, Jonas, Bøggild, Thomas, Wang, Xi, Lin, Long, Nursyifa, Casia, Liu, Xiaodong, Li, Zilong, Chege, Mumbi, Moodley, Yoshan, Brüniche-Olsen, Anna, Kuja, Josiah, Schubert, Mikkel, Agaba, Morris, Santander, Cindy G., Sinding, Mikkel Holger S., Muwanika, Vincent, Masembe, Charles, Siegismund, Hans R., Moltke, Ida, Albrechtsen, Anders, and Heller, Rasmus

Abstract

Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations., Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.

Published
2024

28. 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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30. The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge

Author

Lin, Audrey T., primary, Hammond-Kaarremaa, Liz, additional, Liu, Hsiao-Lei, additional, Stantis, Chris, additional, McKechnie, Iain, additional, Pavel, Michael, additional, Pavel, Susan sa'hLa mitSa, additional, Wyss, Senaqwila Sen̓áḵw, additional, Sparrow, Debra qwasen, additional, Carr, Karen, additional, Aninta, Sabhrina Gita, additional, Perri, Angela, additional, Hartt, Jonathan, additional, Bergström, Anders, additional, Carmagnini, Alberto, additional, Charlton, Sophy, additional, Dalén, Love, additional, Feuerborn, Tatiana R., additional, France, Christine A. M., additional, Gopalakrishnan, Shyam, additional, Grimes, Vaughan, additional, Harris, Alex, additional, Kavich, Gwénaëlle, additional, Sacks, Benjamin N., additional, Sinding, Mikkel-Holger S., additional, Skoglund, Pontus, additional, Stanton, David W. G., additional, Ostrander, Elaine A., additional, Larson, Greger, additional, Armstrong, Chelsey G., additional, Frantz, Laurent A. F., additional, Hawkins, Melissa T. R., additional, and Kistler, Logan, additional

Published
2023
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31. Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

Author

Chen, Ningbo, primary, Zhang, Zhengwei, additional, Hou, Jiawen, additional, Chen, Jialei, additional, Gao, Xuan, additional, Tang, Li, additional, Wangdue, Shargan, additional, Zhang, Xiaoming, additional, Sinding, Mikkel-Holger S., additional, Liu, Xuexue, additional, Han, Jianlin, additional, Lü, Hongliang, additional, Lei, Chuzhao, additional, Marshall, Fiona, additional, and Liu, Xinyi, additional

Published
2023
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32. Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations

Author

von Seth, Johanna, Dussex, Nicolas, Díez-del-Molino, David, van der Valk, Tom, Kutschera, Verena E., Kierczak, Marcin, Steiner, Cynthia C., Liu, Shanlin, Gilbert, M. Thomas P., Sinding, Mikkel-Holger S., Prost, Stefan, Guschanski, Katerina, Nathan, Senthilvel K. S. S., Brace, Selina, Chan, Yvonne L., Wheat, Christopher W., Skoglund, Pontus, Ryder, Oliver A., Goossens, Benoit, Götherström, Anders, and Dalén, Love

Published
2021
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33. Population genomics of the muskox' resilience in the near absence of genetic variation

Author

Pečnerová, Patrícia, primary, Lord, Edana, additional, Garcia‐Erill, Genís, additional, Hanghøj, Kristian, additional, Rasmussen, Malthe Sebro, additional, Meisner, Jonas, additional, Liu, Xiaodong, additional, van der Valk, Tom, additional, Santander, Cindy G., additional, Quinn, Liam, additional, Lin, Long, additional, Liu, Shanlin, additional, Carøe, Christian, additional, Dalerum, Fredrik, additional, Götherström, Anders, additional, Måsviken, Johannes, additional, Vartanyan, Sergey, additional, Raundrup, Katrine, additional, Al‐Chaer, Amal, additional, Rasmussen, Linett, additional, Hvilsom, Christina, additional, Heide‐Jørgensen, Mads Peter, additional, Sinding, Mikkel‐Holger S., additional, Aastrup, Peter, additional, Van Coeverden de Groot, Peter J., additional, Schmidt, Niels Martin, additional, Albrechtsen, Anders, additional, Dalén, Love, additional, Heller, Rasmus, additional, Moltke, Ida, additional, and Siegismund, Hans Redlef, additional

Published
2023
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35. 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

37. Greenland sled dogs at risk of extinction

Author

Sills, Jennifer, Sonne, Christian, Langebæk, Rikke, Dietz, Rune, Andersen-Ranberg, Emilie, Houser, Geoff, Hansen, Anders J., Sinding, Mikkel-Holger S., Olsen, Morten Tange, Egevang, Carsten, Gilbert, M. Thomas P., and Meldgaard, Morten

Published
2018

39. Sled Dogs as Sentinel Species for Monitoring Arctic Ecosystem Health

Author

Sonne, Christian, primary, Letcher, Robert J., additional, Jenssen, Bjørn M., additional, Desforges, Jean-Pierre, additional, Eulaers, Igor, additional, Andersen-Ranberg, Emilie, additional, Gustavson, Kim, additional, Bossi, Rosanna, additional, Styrishave, Bjarne, additional, Sinding, Mikkel-Holger S., additional, and Dietz, Rune, additional

Published
2019
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41. African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Author

Balboa, Renzo F., primary, Bertola, Laura D., additional, Brüniche-Olsen, Anna, additional, Rasmussen, Malthe Sebro, additional, Liu, Xiaodong, additional, Besnard, Guillaume, additional, Salmona, Jordi, additional, Santander, Cindy G., additional, He, Shixu, additional, Zinner, Dietmar, additional, Pedrono, Miguel, additional, Muwanika, Vincent, additional, Masembe, Charles, additional, Schubert, Mikkel, additional, Kuja, Josiah, additional, Quinn, Liam, additional, Garcia-Erill, Genís, additional, Rakotoarivony, Rianja, additional, Henrique, Margarida, additional, Lin, Long, additional, Wang, Xi, additional, Heaton, Michael P., additional, Smith, Timothy P. L., additional, Hanghøj, Kristian, additional, Sinding, Mikkel-Holger S., additional, Atickem, Anagaw, additional, Chikhi, Lounès, additional, Roos, Christian, additional, Gaubert, Philippe, additional, Siegismund, Hans R., additional, Moltke, Ida, additional, Albrechtsen, Anders, additional, and Heller, Rasmus, additional

Published
2023
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42. Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole‐genome sequencing

Author

Hernández‐Alonso, Germán, primary, Ramos‐Madrigal, Jazmín, additional, Sun, Xin, additional, Scharff‐Olsen, Camilla Hjorth, additional, Sinding, Mikkel‐Holger S., additional, Martins, Nuno F., additional, Ciucani, Marta Maria, additional, Mak, Sarah S. T., additional, Lanigan, Liam Thomas, additional, Clausen, Cecilie G., additional, Bhak, Jong, additional, Jeon, Sungwon, additional, Kim, Changjae, additional, Eo, Kyung Yeon, additional, Cho, Seong‐Ho, additional, Boldgiv, Bazartseren, additional, Gantulga, Gankhuyag, additional, Unudbayasgalan, Zunduibaatar, additional, Kosintsev, Pavel A., additional, Stenøien, Hans K., additional, Gilbert, M. Thomas P., additional, and Gopalakrishnan, Shyam, additional

Published
2023
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44. A 5700 year-old human genome and oral microbiome from chewed birch pitch

Author

Jensen, Theis Z. T., Niemann, Jonas, Iversen, Katrine Højholt, Fotakis, Anna K., Gopalakrishnan, Shyam, Vågene, Åshild J., Pedersen, Mikkel Winther, Sinding, Mikkel-Holger S., Ellegaard, Martin R., Allentoft, Morten E., Lanigan, Liam T., Taurozzi, Alberto J., Nielsen, Sofie Holtsmark, Dee, Michael W., Mortensen, Martin N., Christensen, Mads C., Sørensen, Søren A., Collins, Matthew J., Gilbert, M. Thomas P., Sikora, Martin, Rasmussen, Simon, and Schroeder, Hannes

Published
2019
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47. “Type D” killer whale genomes reveal long-term small population size and low genetic diversity

Author

Foote, Andrew D, primary, Alexander, Alana, additional, Ballance, Lisa T, additional, Constantine, Rochelle, additional, Galletti Vernazzani Muñoz, Bárbara, additional, Guinet, Christophe, additional, Robertson, Kelly M, additional, Sinding, Mikkel-Holger S, additional, Sironi, Mariano, additional, Tixier, Paul, additional, Totterdell, John, additional, Towers, Jared R, additional, Wellard, Rebecca, additional, Pitman, Robert L, additional, and Morin, Phillip A, additional

Published
2023
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48. The history of Coast Salish 'woolly dogs' revealed by ancient genomics and Indigenous Knowledge

Author

Lin, Audrey T., Hammond-Kaarremaa, Liz, Liu, Hsiao-Lei, Stantis, Chris, McKechnie, Iain, Pavel, Michael, Pavel, Susan Sa'hLa MitSa, Wyss, Senaqwila Sen̓áḵw, Sparrow, Debra Qwasen, Carr, Karen, Aninta, Sabhrina Gita, Perri, Angela, Hartt, Jonathan, Bergström, Anders, Carmagnini, Alberto, Charlton, Sophy, Dalén, Love, Feuerborn, Tatiana R., France, Christine A. M., Gopalakrishnan, Shyam, Grimes, Vaughan, Harris, Alex, Kavich, Gwénaëlle, Sacks, Benjamin N., Sinding, Mikkel-Holger S., Skoglund, Pontus, Stanton, David W. G., Ostrander, Elaine A., Larson, Greger, Armstrong, Chelsey G., Frantz, Laurent A. F., Hawkins, Melissa T. R., Kistler, Logan, Lin, Audrey T., Hammond-Kaarremaa, Liz, Liu, Hsiao-Lei, Stantis, Chris, McKechnie, Iain, Pavel, Michael, Pavel, Susan Sa'hLa MitSa, Wyss, Senaqwila Sen̓áḵw, Sparrow, Debra Qwasen, Carr, Karen, Aninta, Sabhrina Gita, Perri, Angela, Hartt, Jonathan, Bergström, Anders, Carmagnini, Alberto, Charlton, Sophy, Dalén, Love, Feuerborn, Tatiana R., France, Christine A. M., Gopalakrishnan, Shyam, Grimes, Vaughan, Harris, Alex, Kavich, Gwénaëlle, Sacks, Benjamin N., Sinding, Mikkel-Holger S., Skoglund, Pontus, Stanton, David W. G., Ostrander, Elaine A., Larson, Greger, Armstrong, Chelsey G., Frantz, Laurent A. F., Hawkins, Melissa T. R., and Kistler, Logan

Abstract

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired woolly dogs that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton", collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Published
2023
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49. Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla)

Author

Hansen, Charles Christian Riis, Láruson, Áki Jarl, Rasmussen, Jacob Agerbo, Ballesteros, Jesus Adrian Chimal, Sinding, Mikkel-Holger S., Hallgrimsson, Gunnar T., von Schmalensee, Menja, Stefansson, Robert A., Skarphédinsson, Kristinn Haukur, Labansen, Aili Lage, Leivits, Madis, Sonne, Christian, Dietz, Rune, Skelmose, Kim, Boertmann, David, Eulaers, Igor, Martin, Michael D., Helgason, Agnar S., Gilbert, M. Thomas P., Pálsson, Snæbjörn, Hansen, Charles Christian Riis, Láruson, Áki Jarl, Rasmussen, Jacob Agerbo, Ballesteros, Jesus Adrian Chimal, Sinding, Mikkel-Holger S., Hallgrimsson, Gunnar T., von Schmalensee, Menja, Stefansson, Robert A., Skarphédinsson, Kristinn Haukur, Labansen, Aili Lage, Leivits, Madis, Sonne, Christian, Dietz, Rune, Skelmose, Kim, Boertmann, David, Eulaers, Igor, Martin, Michael D., Helgason, Agnar S., Gilbert, M. Thomas P., and Pálsson, Snæbjörn

Abstract

Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: (1) Isolation of refugia during the last glacial period 110–115,000 years ago, (2) population divergence following the colonization of the deglaciated areas ~10,000 years ago, (3) human population expansion, which led to the settlement in Iceland ~1100 years ago, and (4) human persecution and exposure to toxic pollutants during the last two centuries.

Published
2023

50. “Type D” killer whale genomes reveal long-term small population size and low genetic diversity

Author

Foote, Andrew D, Alexander, Alana, Ballance, Lisa T, Constantine, Rochelle, Galletti Vernazzani Muñoz, Bárbara, Guinet, Christophe, Robertson, Kelly M, Sinding, Mikkel-holger S, Sironi, Mariano, Tixier, Paul, Totterdell, John, Towers, Jared R, Wellard, Rebecca, Pitman, Robert L, Morin, Phillip A, Foote, Andrew D, Alexander, Alana, Ballance, Lisa T, Constantine, Rochelle, Galletti Vernazzani Muñoz, Bárbara, Guinet, Christophe, Robertson, Kelly M, Sinding, Mikkel-holger S, Sironi, Mariano, Tixier, Paul, Totterdell, John, Towers, Jared R, Wellard, Rebecca, Pitman, Robert L, and Morin, Phillip A

Abstract

Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations.

Published
2023
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