Papers

2025

AR Barton, CG Santander, P Skoglund, I Moltke, D Reich, I Mathieson (2025) Insufficient evidence for natural selection associated with the Black Death, Nature, DOI: 10.1038/s41586-024-08496-5

L Saag, O Utevska, S Zadnikov, I Shramko, K Gorbenko, M Bandrivskyi, D Pavliv, I Bruyako, D Grechko, V Okatenko, G Toshev, S Andrukh, V Radziyevska, Y Buynov, V Kotenko, O Smyrnov, O Petrauskas, B Magomedov, S Didenko, A Heiko, R Reida, S Sapiehin, V Aksonov, O Laptiev, S Terskyi, V Skorokhod, V Zhyhola, Y Sytyi, M Järve, C Scheib, K Anastasiadou, M Kelly, M Williams, M Silva, C Barrington, A Gilardet, R Macleod, P Skoglund, M Thomas (2025) North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period, Science Advances, 11:eadr0695

L Speidel, M Silva, T Booth, B Raffield, K Anastasiadou, C Barrington, A Götherström, P Heather, P Skoglund (2025) High-resolution genomic history of early medieval Europe, Nature, 637:118–126 

2024

P Swali, T Booth, CC Tan, J McCabe, K Anastasiadou, C Barrington, M Borrini, A Bricking, J Buckberry, L Büster, R Carlin, A Gilardet, I Glocke, J Irish, M Kelly, M King, F Petchey, J Peto, M Silva, L Speidel, F Tait, A Teoaca, V Valoriani, M Williams, R Madgwick, G Mullan, L Wilson, K Cootes, I Armit, MG Gutierrez, L van Dorp, P Skoglund (2024) Ancient Borrelia genomes document the evolutionary history of louse-borne relapsing fever, bioRxiv preprint, https://doi.org/10.1101/2024.07.18.603748 

CT Stankey, C Bourges, LM Haag, T Turner-Stokes, AP Piedade, C Palmer-Jones, I Papa, M Silva dos Santos, Q Zhang, AJ Cameron, A Legrini, T Zhang, CS Wood, FN New, LO Randzavola, L Speidel, AC Brown, A Hall, F Saffioti, EC Parkes, W Edwards, H Direskeneli, PC Grayson, L Jiang, PA Merkel, G Saruhan-Direskeneli, AH Sawalha, E Tombetti, A Quaglia, D Thorburn, JC Knight, AP Rochford, CD Murray, P Divakar, M Green, E Nye, JI MacRae, NB Jamieson, P Skoglund, MZ Cader, C Wallace, DC Thomas, JC Lee (2024) A disease-associated gene desert directs macrophage inflammation through ETS2, Nature, 630:447–456

K Anastasiadou, M Silva, T Booth, L Speidel, T Audsley, C Barrington, J Buckberry, D Fernandes, B Ford, M Gibson, A Gilardet, I Glocke, K Keefe, M Kelly, M Masters, J McCabe, L McIntyre, P Ponce, S Rowland, J Ruiz Ventura, P Swali, F Tait, D Walker, H Webb, M Williams, A Witkin, M Holst, L Loe, I Armit, R Schulting, P Skoglund (2024) Detection of chromosomal aneuploidy in ancient genomes, Communications Biology, 7:14

M Silva, T Booth, J Moore, K Anastasiadou, D Walker, A Gilardet, C Barrington, M Kelly, M Williams, M Henderson, A Smith, D Bowsher, J Montgomery, P Skoglund (2024) An individual with Sarmatian-related ancestry in Roman Britain. Current Biology, 34:1-9

2023

P Swali, R Schulting, A Gilardet, M Kelly, K Anastasiadou, I Glocke, J McCabe, M Williams, T Audsley, L Loe, T Fernández-Crespo, J Ordoño, D Walker, T Clare, G Cook, I Hodkinson, M Simpson, S Read, T Davy, M Silva, M Hajdinjak, A Bergström, T Booth, P Skoglund (2023) Yersinia pestis genomes reveal plague in Britain 4,000 years ago, Nature Communications, DOI:10.1038/s41467-023-38393-w

T Davy, D Ju, I Mathieson$, P Skoglund$ (2023) Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers, Current Biology, 33(7):1365-1371.e3

R Rodríguez-Varela, KHS Moore, S Ebenesersdóttir, G Merve-Kilinc, A Kjellström, L Papmehl-Dufay, C Alfsdotter, B Berglund, L Alrawi, N Kashuba, V Sobrado, V Kempe Lagerholm, E Gilbert, GL Cavalleri, E Hovig, I Kockum, T Olsson, L Alfredsson, TF Hansen, T Werge, AR Munters. C Bernhardsson, B Skar, A Christophersen, G Turner-Walker, S Gopalakrishnan, E Daskalaki, A Omrak, P Pérez-Ramallo, P Skoglund, L Girdland-Flink, F Gunnarsson, C Hedenstierna-Jonson, MTP Gilbert, K Lidén, M Jakobsson, L Einarsson, H Victor, M Krzewińska, T Zachrisson, J Storå, K Stefánsson, A Helgason, A Götherström (2023) The genetic history of Scandinavia from the Roman Iron Age to the present, Cell, 186(1):32-46.e19

2022

S Charlton* , S Brace*, M Hajdinjak*, R Kearney, T Booth, H Reade, JA Tripp, KL Sayle, SB Grimm, SM Bello, EA Walker, A Gilardet, P East, I Glocke, G Larson, T Higham, C Stringer, P Skoglund$, I Barnes$, RE Stevens$ (2022) Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain, Nature Ecology & Evolution, DOI: 10.1038/s41559-022-01883-z

A Bergström*, DWG Stanton*, UH Taron*, L Frantz, MHS Sinding, E Ersmark, S Pfrengle, M Cassatt-Johnstone, O Lebrasseur, L Girdland-Flink, DM Fernandes, M Ollivier, L Speidel, S Gopalakrishnan, MV Westbury, J Ramos-Madrigal, TR Feuerborn, E Reiter, J Gretzinger, SC. Münzel, P Swali, N Conard, C Carøe, J Haile, A Linderholm, S Androsov, I Barnes, C Baumann, N Benecke, H Bocherens, S Brace, RF Carden, DG Drucker, S Fedorov, M Gasparik, M Germonpré, S Grigoriev, P Groves, ST Hertwig, VV Ivanova, L Janssens, RP Jennings, AK Kasparov, IV Kirrilova, I Kurmaniyazov, YV Kuzmin, PA Kosintsev, M Lázničková-Galetová, C Leduc, P Nikolskiy, M Nussbaumer, C O'Drisceoil, L Orlando, A Outram, EY. Pavlova, AR Perri, M Pilot, VV Pitulko, V Plotnikov, A Protopopov, A Rehazek, M Sablin, A Seguin-Orlando, J Storå, C Verjux, VF Zaibert, G Zazula, P Crombé, A Hansen, E Willerslev, JA Leonard, A Götherström, R Pinhasi, VJ Schuenemann, M Hofreiter, MTP Gilbert, B Shapiro, G Larson, J Krause, L Dalén, P Skoglund (2022) Gray wolf genomic history reveals a dual ancestry of dogs, Nature, 607:313–320 [PDF]

A Bergström, P Skoglund (2022) Ice Age wolf genomes home in on dog origins, Nature, DOI:10.1038/d41586-022-01551-z

2021

A Picin, S Benazzi, R Blasco, M Hajdinjak, KM Helgen, J-J Hublin, J Rosell, P Skoglund, C Stringer, S Talamo (2021) Comment on “A global environmental crisis 42,000 years ago”, Science, 374:6570

S Alpaslan-Roodenberg, D Anthony, H Babiker, E Bánffy, T Booth, P Capone, A Deshpande-Mukherjee, S Eisenmann, L Fehren-Schmitz, M Frachetti, R Fujita, CJ Frieman, Q Fu, V Gibbon, W Haak, M Hajdinjak, KP Hofmann, B Holguin, T Inomata, H Kanzawa-Kiriyama, W Keegan, J Kelso, J Krause, G Kumaresan, C Kusimba, S Kusimba, C Lalueza-Fox, B Llamas, S MacEachern, S Mallick, H Matsumura, AY Morales-Arce, G M Matuzeviciute, V Mushrif-Tripathy, N Nakatsuka, R Nores, C Ogola, M Okumura, N Patterson, R Pinhasi, SPR Prasad, ME Prendergast, JL Punzo, D Reich, R Sawafuji, E Sawchuk, S Schiffels, J Sedig, S Shnaider, K Sirak, P Skoglund, V Slon, M Snow, M Soressi, M Spriggs, PW Stockhammer, A Szécsényi-Nagy, K Thangaraj, V Tiesler, R Tobler, CC Wang, C Warinner, S Yasawardene, M Zahir (2021) Ethics of DNA research on human remains: five globally applicable guidelines, Nature,  DOI: 10.1038/s41586-021-04008-x

L Speidel, L Cassidy, RW Davies, G Hellenthal, P Skoglund, S Myers (2021) Inferring population histories for ancient genomes using genome-wide genealogies, Molecular Biology and Evolution, 38(9)3497–3511

P Gelabert*, S Sawyer*, A Bergström*, T C Collin, T Meshvelian, A Belfer-Cohen, D Lordkipanidze, N Jakeli, Z Matskevich, G Bar-Oz, DM Fernandes, O Cheronet, KT Ozdogan, V Oberreiter, RNM Feeney, P Skoglund§, R Pinhasi§ (2021) Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment, Current Biology, 31:1-11

J Von Seth, N Dussex, D Díez-del-Molino, T Van Der Valk, VE Kutschera, M Kierczak, CC Steiner, S Liu, MTP Gilbert, M-HS Sinding, S Prost, K Guschanski, SKSS Nathan, S Brace, YL Chan, CW Wheat, Pontus Skoglund, OA Ryder, B Goossens, A Götherström, L Dalén (2021) Genomic insights into the conservation status of the world’s last remaining Sumatran rhinoceros populations, Nature Communications, 12(1):1-11

M Hajdinjak, F Mafessoni, L Skov, B Vernot, A Hübner, Q Fu, E Essel, S Nagel, B Nickel, J Richter, O Teodora Moldovan, S Constantin, E Endarova, N Zahariev, R Spasov, F Welker, GM Smith, V Sinet-Mathiot, L Paskulin, H Fewlass, S Talamo, Z Rezek, S Sirakova, N Sirakov, SP McPherron, T Tsanova, J-J Hublin, BM Peter, M Meyer, P Skoglund, J Kelso, S Pääbo (2021) Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry, Nature, 592:253–257

T van der Valk*, P Pečnerová*, D Díez-del-Molino*, A Bergström, J Oppenheimer, S Hartmann, G Xenikoudakis, JA Thomas, M Dehasque, E Sağlıcan, F Rabia Fidan, I Barnes, S Liu, M Somel, PD Heintzman, P Nikolskiy, B Shapiro, P Skoglund, M Hofreiter, AM Lister, A Götherström§, L Dalén§ (2021) Million-year-old DNA sheds light on the genomic history of mammoths, Nature, https://doi.org/10.1038/s41586-021-03224-9

A Bergström, C Stringer, M Hajdinjak, E Scerri, P Skoglund (2021) Origins of modern human ancestry, Nature, 590:229–237

L Orlando, R Allaby, P Skoglund, C Der Sarkissian, PW Stockhammer, MC Ávila-Arcos, Q Fu, J Krause, E Willerslev, AC Stone, C Warinner (2021) Ancient DNA analysis. Nature Reviews Methods Primers, 1:14  [PDF]

2020

A Bergström, L Frantz, R Schmidt, E Ersmark, O Lebrasseur, L Girdland-Flink, AT Lin, J Storå, K-G Sjögren, D Anthony, E Antipina, S Amiri, G Bar-Oz, VI Bazaliiskii, J Bulatovic, D Brown, A Carmagnini, T Davy, S Fedorov, I Fiore, D Fulton, M Germonpré, J Haile, EK Irving-Pease, A Jamieson, L Janssens, I Kirillova, L Kolska Horwitz, J Kuzmanovic-Cvetkovic, Y Kuzmin, RJ Losey, D Ložnjak Dizdar, M Mashkour, M Novak, V Onar, D Orton, M Pasaric, M Radivojevic, D Rajkovic, B Roberts, H Ryan, M Sablin, F Shidlovskiy, I Stojanovic, A Tagliacozzo, K Trantalidou, I Ullén, A Villaluenga, P Wapnish, K Dobney, A Götherström, A Linderholm, L Dalén, R Pinhasi, G Larson, P Skoglund (2020) Origins and genetic legacy of prehistoric dogs, Science, 370(6516):557-564 [PDF] [Supplementary Material] [Data]

DWG Stanton, F Alberti, V Plotnikov, S Androsov, S Grigoriev, S Fedorov, P Kosintsev, D Nagel, S Vartanyan, I Barnes, R Barnett, E Ersmark, D Döppes, M Germonpré, M Hofreiter, W Rosendahl, P Skoglund, L Dalén (2020) Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion, Scientific Reports, 10:12621

MS Sinding, S Gopalakrishnan, J Ramos-Madrigal, M de Manuel, VV Pitulko, L Kuderna, TR Feuerborn, LAF Frantz, FG Vieira, J Niemann, JA Samaniego Castruita, C Carøe, EU Andersen-Ranberg, PD Jordan, EY Pavlova, PA Nikolskiy, AK Kasparov, VV Ivanova, E Willerslev, P Skoglund, M Fredholm, SE Wennerberg, MP Heide-Jørgensen, R Dietz, C Sonne, M Meldgaard, L Dalén, G Larson, B Petersen, T Sicheritz-Pontén, L Bachmann, Ø Wiig, T Marques-Bonet, AJ Hansen, MTP Gilbert (2020) Arctic-adapted dogs emerged at the Pleistocene–Holocene transition, Science, 368(6498):1495-1499

F Mafessoni, S Grote, C de Filippo, V Slon, KA Kolobova, B Viola, S Markin, M Chintalapati, S Peyrégne, L Skov, P Skoglund, AI Krivoshapkin, AP Derevianko, M Meyer, J Kelso, B Peter, K Prüfer, S Pääbo (2020) A high-coverage Neandertal genome from Chagyrskaya Cave, PNAS, 117(26):15132-15136

N Nakatsuka, I Lazaridis, C Barbieri, P Skoglund, N Rohland, S Mallick, C Posth, K Harkins-Kinkaid, M Ferry, É Harney, M Michel, K Stewardson, J Novak-Forst, JM Capriles, M Alfonso Durruty, K Aranda Álvarez, D Beresford-Jones, R Burger, L Cadwallader, R Fujita, J Isla, G Lau, C Lémuz Aguirre, S LeBlanc, SC Maldonado, F Meddens, PG Messineo, BJ Culleton, TK Harper, J Quilter, G Politis, K Rademaker, M Reindel, M Rivera, L Salazar, JR Sandoval, CM Santoro, N Scheifler, V Standen, MI Barreto, I Flores Espinoza, E Tomasto-Cagigao, G Valverde, DJ Kennett, A Cooper, J Krause, W Haak, B Llamas, D Reich, L Fehren-Schmitz (2020) A Paleogenomic Reconstruction of the Deep Population History of the Andes, Cell, 181(5):1131-1145

A Bergström, SA McCarthy, R Hui, MA Almarri, Q Ayub, P Danecek, Y Chen, S Felkel, P Hallast, J Kamm, H Blanché, J-F Deleuze, H Cann, S Mallick, D Reich, MS Sandhu, P Skoglund, A Scally, Y Xue, R Durbin, C Tyler-Smith (2020) Insights into human genetic variation and population history from 929 diverse genomes, Science, 367(6484):eaay5012 [PDF]

I Mathieson, F Abascal, L Vinner, P Skoglund, C Pomilla, P Mitchell, C Arthur, D Gurdasani, E Willerslev, MS Sandhu, G Dewar (2020) An ancient baboon genome demonstrates long-term population continuity in southern Africa. Genome Biology and Evolution, evaa019

2019

G-D Wang, M Zhang, X Wang, MA Yang, P Cao, F Liu, H Lu, X Feng, P Skoglund, L Wang, Q Fu, Y-P Zhang (2019) Genomic Approaches Reveal an Endemic Subpopulation of Gray Wolves in Southern China, iScience, 20:110-118

M Pilot, AE Moura, IM Okhlopkov, NV Mamaev, AN Alagaili, OB Mohammed, EG Yavruyan, NH Manaseryan, VHayrapetyan, N Kopaliani, E Tsingarska, M Krofel, P Skoglund, W Bogdanowicz (2019) Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage, Scientific Reports, 9(1):1-13

P Flegontov, NE Altınışık, P Changmai, N Rohland, S Mallick, N Adamski, DA Bolnick, N Broomandkhoshbacht, F Candilio, BJ Culleton, O Flegontova, TM Friesen, C Jeong, TK Harper, D Keating, DJ Kennett, AM Kim, TC Lamnidis, AM Lawson, I Olalde, J Oppenheimer, BA Potter, J Raff, RA Sattler, P Skoglund, K Stewardson, EJ Vajda, S Vasilyev, E Veselovskaya, MG Hayes, DH O’Rourke, J Krause, R Pinhasi, D Reich, S Schiffels (2019) Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America, Nature, 570:236–240, [PDF]

M Spriggs, F Valentin, S Bedford, R Pinhasi, P Skoglund, D Reich, M Lipson (2019) Revisiting ancient DNA insights into the human history of the Pacific Islands, Archaeology in Oceania, DOI: 10.1002/arco.5180 

2018

C Posth*, N Nakatsuka*, I Lazaridis, P Skoglund,  S Mallick, TC Lamnidis, N Rohland, K Nägele, N Adamski, E Bertolini, N Broomandkhoshbacht, A Cooper, BJ Culleton, T Ferraz, M Ferry, A Furtwängler, W Haak, K Harkins, TK Harper, T Hünemeier, AM Lawson, B Llamas, M Michel, E Nelson, J Oppenheimer, N Patterson, S Schiffels, J Sedig,  K Stewardson, S Talamo, C-C Wang, J-J Hublin, M Hubbe, K Harvati, A Nuevo Delaunay, J Beier, M Francken, P Kaulicke, H Reyes-Centeno, K Rademaker, WR Trask, M Robinson, SM Gutierrez, KM Prufer, DC Salazar-Garcia, E Nunes Chim, L Müller Plumm Gomes, M Lopes Alves, A Liryo, M Inglez, R Elias Oliveira, DV Bernardo, A Barioni, V Wesolowski, NA Scheifler, MA Rivera, CR Plens, PG Messineo, L Figuti, D Corach, C Scabuzzo, S Eggers, P DeBlasis, M Reindel, C Méndez, G Politis, E Tomasto-Cagigao, DJ Kennett, A Strauss, L Fehren-Schmitz, J Krause, D Reich (2018) Reconstructing the Deep Population History of Central and South America, Cell, 175(5):1185-1197.e22

K Tambets, B Yunusbayev, G Hudjashov, A-M Ilumäe, S Rootsi, T Honkola, O Vesakoski, Q Atkinson, P Skoglund, A Kushniarevich, S Litvinov, M Reidla, E Metspalu, L Saag, T Rantanen, M Karmin, J Parik, SI Zhadanov, M Gubina, LD Damba, M Bermisheva, T Reisberg, K Dibirova, I Evseeva, M Nelis, J Klovins, A Metspalu, T Esko, O Balanovsky, E Balanovska, EK Khusnutdinova, LP Osipova, M Voevoda, R Villems, T Kivisild, M Metspalu (2018) Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations, Genome Biology 19:139

P Skoglund, I Mathieson (2018), Ancient human genomics: the first decade. Annual Review of Genomics and Human Genetics, 19:8.1–8.24, [PDF]

P Skoglund, S Mallick, N Patterson, D Reich (2018) No evidence for unknown archaic ancestry in South Asia. Nature Genetics, 50:632–633

M Hajdinjak, Q Fu, A Hübner, M Petr, F Mafessoni, S Grote, P Skoglund, V Narasimham, H Rougier, I Crevecoeur, P Semal, M Soressi, S Talamo, J-J Hublin, I Gušić, Ž Kućan, P Rudan, LV Golovanova, VB Doronichev, C Posth, J Krause, P Korlević, S Nagel, B Nickel, M Slatkin, N Patterson,  D Reich, K Prüfer, M Meyer, S Pääbo§, J Kelso§ (2018) Reconstructing the genetic history of late Neanderthals, Nature, 555, 652–656

P Skoglund (2018) Northwest Passage to Scandinavia, Nature Ecology & Evolution, 2:593–594 [PDF]

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Pontus' full publication list including prior to founding the lab: https://scholar.google.com/citations?user=KJcADbYAAAAJ&hl=en 

*These authors contributed equally/co-first authors

§These authors contributed equally/co-senior authors