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5. Cover

Author

Haile, James B.

Published
2020

6. Index

Author

Haile, James B.

Published
2020

10. Notes

Author

Haile, James B.

Published
2020

20. 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

21. 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

23. Millennial-scale variations in Arctic sea ice are recorded in sedimentary ancient DNA of the microalga Polarella glacialis

Author

Harðardóttir, Sara, Haile, James S., Ray, Jessica Louise, Limoges, Audrey, Van Nieuwenhove, Nicolas, Lalande, Catherine, Grondin, Pierre-Luc, Jackson, Rebecca, Skaar, Katrine Sandnes, Heikkilä, Maija, Berge, Jørgen, Lundholm, Nina, Massé, Guillaume, Rysgaard, Søren, Seidenkrantz, Marit-Solveig, De Schepper, Stijn, Lorenzen, Eline D., Lovejoy, Connie, and Ribeiro, Sofia

Published
2024
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24. Reply to: When did mammoths go extinct?

Author

Wang, Yucheng, Prohaska, Ana, Dong, Haoran, Alberti, Adriana, Alsos, Inger Greve, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Cherezova, Anna A., Coissac, Eric, De Sanctis, Bianca, Denoeud, France, Dockter, Christoph, Durbin, Richard, Edwards, Mary E., Edwards, Neil R., Esdale, Julie, Fedorov, Grigory B., Fernandez-Guerra, Antonio, Froese, Duane G., Gusarova, Galina, Haile, James, Holden, Philip B., Kjeldsen, Kristian K., Kjær, Kurt H., Korneliussen, Thorfinn Sand, Lammers, Youri, Larsen, Nicolaj Krog, Macleod, Ruairidh, Mangerud, Jan, McColl, Hugh, Merkel, Marie Kristine Føreid, Money, Daniel, Möller, Per, Nogués-Bravo, David, Orlando, Ludovic, Owens, Hannah Lois, Pedersen, Mikkel Winther, Racimo, Fernando, Rahbek, Carsten, Rasic, Jeffrey T., Rouillard, Alexandra, Ruter, Anthony H., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Vinner, Lasse, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Meltzer, David J., and Willerslev, Eske

Published
2022
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26. 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

27. 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

29. Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Author

Wang, Yucheng, Pedersen, Mikkel Winther, Alsos, Inger Greve, De Sanctis, Bianca, Racimo, Fernando, Prohaska, Ana, Coissac, Eric, Owens, Hannah Lois, Merkel, Marie Kristine Føreid, Fernandez-Guerra, Antonio, Rouillard, Alexandra, Lammers, Youri, Alberti, Adriana, Denoeud, France, Money, Daniel, Ruter, Anthony H., McColl, Hugh, Larsen, Nicolaj Krog, Cherezova, Anna A., Edwards, Mary E., Fedorov, Grigory B., Haile, James, Orlando, Ludovic, Vinner, Lasse, Korneliussen, Thorfinn Sand, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Dockter, Christoph, Esdale, Julie, Gusarova, Galina, Kjeldsen, Kristian K., Mangerud, Jan, Rasic, Jeffrey T., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Froese, Duane G., Rahbek, Carsten, Bravo, David Nogues, Holden, Philip B., Edwards, Neil R., Durbin, Richard, Meltzer, David J., Kjær, Kurt H., Möller, Per, and Willerslev, Eske

Published
2021
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30. 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

33. 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

34. 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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35. Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

Author

Soares, André ER, Novak, Ben J, Haile, James, Heupink, Tim H, Fjeldså, Jon, Gilbert, M Thomas P, Poinar, Hendrik, Church, George M, and Shapiro, Beth

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Generic health relevance, Animals, Base Sequence, Bayes Theorem, Biological Evolution, Columbidae, Extinction, Biological, Genetic Variation, Genome, Mitochondrial, High-Throughput Nucleotide Sequencing, Phylogeny, Sequence Analysis, DNA, Ancient DNA, time calibrated phylogeny, Pezophaps solitaria, Raphus cucullatus, Passenger pigeon, Ecology, Evolutionary biology
Abstract

BackgroundPigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context.ResultsWe used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves.ConclusionsOur analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.

Published
2016

36. Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Author

Wang, Yucheng, Pedersen, Mikkel Winther, Alsos, Inger Greve, De Sanctis, Bianca, Racimo, Fernando, Prohaska, Ana, Coissac, Eric, Owens, Hannah Lois, Merkel, Marie Kristine Føreid, Fernandez-Guerra, Antonio, Rouillard, Alexandra, Lammers, Youri, Alberti, Adriana, Denoeud, France, Money, Daniel, Ruter, Anthony H., McColl, Hugh, Larsen, Nicolaj Krog, Cherezova, Anna A., Edwards, Mary E., Fedorov, Grigory B., Haile, James, Orlando, Ludovic, Vinner, Lasse, Korneliussen, Thorfinn Sand, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Dockter, Christoph, Esdale, Julie, Gusarova, Galina, Kjeldsen, Kristian K., Mangerud, Jan, Rasic, Jeffrey T., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Froese, Duane G., Rahbek, Carsten, Bravo, David Nogues, Holden, Philip B., Edwards, Neil R., Durbin, Richard, Meltzer, David J., Kjær, Kurt H., Möller, Per, and Willerslev, Eske

Published
2022
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37. The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters

Author

Pundhir, Sachin, Su, Jinyu, Tapia, Marta, Hansen, Anne Meldgaard, Haile, James Seymour, Hansen, Klaus, and Porse, Bo Torben

Subjects
Genetics, Genetics (clinical)
Abstract

SWI/SNF and NuRD are protein complexes that antagonistically regulate DNA accessibility. However, repression of theiractivities often leads to unanticipated changes in target gene expression (paradoxical), highlighting our incomplete understandingof their activities. Here we show that SWI/SNF and NuRD are in a tug-of-war to regulate PRC2 occupancy at lowlyexpressed and bivalent genes in mouse embryonic stem cells (mESCs). In contrast, at promoters of average or highly expressedgenes, SWI/SNF and NuRD antagonistically modulate RNA polymerase II (Pol II) release kinetics, arguably owingto accompanying alterations in H3.3 and H2A.Z levels at promoter-flanking nucleosomes, leading to paradoxical changes ingene expression. Owing to this mechanism, the relative activities of the two remodelers potentiate gene promoters towardPol II–dependent open or PRC2-dependent closed chromatin states. Our results highlight RNA Pol II occupancy as the keyparameter in determining the direction of gene expression changes in response to SWI/SNF and NuRD inactivation at genepromoters in mESCs. SWI/SNF and NuRD are protein complexes that antagonistically regulate DNA accessibility. However, repression of their activities often leads to unanticipated changes in target gene expression (paradoxical), highlighting our incomplete understanding of their activities. Here we show that SWI/SNF and NuRD are in a tug-of-war to regulate PRC2 occupancy at lowly expressed and bivalent genes in mouse embryonic stem cells (mESCs). In contrast, at promoters of average or highly expressed genes, SWI/SNF and NuRD antagonistically modulate RNA polymerase II (Pol II) release kinetics, arguably owing to accompanying alterations in H3.3 and H2A.Z levels at promoter-flanking nucleosomes, leading to paradoxical changes in gene expression. Owing to this mechanism, the relative activities of the two remodelers potentiate gene promoters toward Pol II–dependent open or PRC2-dependent closed chromatin states. Our results highlight RNA Pol II occupancy as the key parameter in determining the direction of gene expression changes in response to SWI/SNF and NuRD inactivation at gene promoters in mESCs.

Published
2023

38. Thelonious.

Author

Haile, James

Subjects
MUSICIANS
Abstract

This article titled "Thelonious" delves into the black experience and philosophy, focusing on the life and influence of Paulin Hountondji, a prominent philosopher from Benin who advocated for Africa's theoretical sovereignty. It also introduces Thelonious, a musician who challenges conventional notions of music by playing without an instrument, prompting readers to contemplate the essence of being a musician and the role of sound. The article emphasizes the significance of African thought and pays tribute to Hountondji's legacy. It further explores a group of individuals striving for black sovereignty and independence, discussing their efforts to establish a new nation through meetings and discussions. The text also examines the concept of freedom and the power of music and sound in expressing and communicating ideas. While initially skeptical, the protagonist becomes immersed in the movement and gains a deeper understanding of its importance. The article delves into the connection between Thelonious Monk, jazz music, and revolution, highlighting the idea that playing music involves not only the notes but also comprehending the underlying meaning and expressing it through the body. It distinguishes between jazz improvisation and free jazz, emphasizing the body's natural response to music. The text references the impact of Ornette Coleman's music and the significance of genuine improvisation. Additionally, it briefly mentions the Republic of New Africa and the Malcolm X Doctrine, which aimed to establish a new political identity for African Americans. The article explores various aspects of the Republic of New Afrika, including its goals of liberation and self [Extracted from the article]

Published
2024

39. 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

40. 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

41. Ancient DNA from sediments and associated remains

Author

Haile, James Seymour, Alan, Cooper, Beth, Shapiro, Cristian, Capelli, and Eske, Willerslev

Subjects
930.1, Biology, Paleontology, Genetics (life sciences), Zoological sciences, aDNA ancient DNA phylogeography phylogenetics
Abstract

This thesis explores the potential of new substrates for ancient DNA studies and addresses novel questions that can now be asked. It also highlights an additional use of ancient DNA extracted from a traditional source.

Published
2008

49. Ancient and modern environmental DNA

Author

Pedersen, Mikkel Winther, Overballe-Petersen, Søren, Ermini, Luca, Der Sarkissian, Clio, Haile, James, Hellstrom, Micaela, Spens, Johan, Thomsen, Philip Francis, Bohmann, Kristine, Cappellini, Enrico, Schnell, Ida Bærholm, Wales, Nathan A., Carøe, Christian, Campos, Paula F., Schmidt, Astrid M. Z., Gilbert, M. Thomas P., Hansen, Anders J., Orlando, Ludovic, and Willerslev, Eske

Published
2015

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