2024

• Lucena-Perez, M., Paijmans, J.L.A., Nocete, F. et al. Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx. Nat Ecol Evol 8, 282–292 (2024). https://doi.org/10.1038/s41559-023-02267-7

2023

• Leedham, Sidney; Paijmans, Johanna LA; Manica, Andrea; Leonardi, Michela (2023) Niche conservatism in a generalist felid: low differentiation of the climatic niche among subspecies of the leopard (Panthera pardus). bioRxiv (): https://doi.org/10.1101/2023.01.26.525491
• Folkertsma, Remco; Charbonnel, Nathalie; Henttonen, Heikki; Heroldova, Marta; Huitu, Otso; Kotlik, Petr; Manzo, Emiliano; Paijmans, Johanna LA; Plantard, Olivier; Sándor, Attila;  (2023) Genomic signatures of climate adaptation in bank voles. (): https://doi.org/10.1002/ece3.10886
• Major, Tom; Renk, Pia; Reissig, Jens; Paijmans, Johanna LA; Morris, Ellie; Hofreiter, Michael; Barlow, Axel; Broadley, Donald G; Wüster, Wolfgang;  (2023) Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe. Plos one 18(9): e0291432. https://doi.org/10.1371/journal.pone.0291432

2022

• Baleka, Sina; Varela, Luciano; Tambusso, P Sebastián; Paijmans, Johanna LA; Mothé, Dimila; Stafford, Thomas W; Fariña, Richard A; Hofreiter, Michael;  (2022) Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA. Iscience 25(1): https://doi.org/10.1016/j.isci.2021.103559
• Lucena-Perez, María; Bazzicalupo, Enrico; Paijmans, Johanna; Kleinman-Ruiz, Daniel; Dalén, Love; Hofreiter, Michael; Delibes, Miguel; Clavero, Miguel; Godoy, Jose A;  (2022) Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe. Quaternary Science Reviews 285(): 107518. https://doi.org/10.1016/j.quascirev.2022.107518
• Agne, Stefanie; Naylor, Gavin JP; Preick, Michaela; Yang, Lei; Thiel, Ralf; Weigmann, Simon; Paijmans, Johanna LA; Barlow, Axel; Hofreiter, Michael; Straube, Nicolas;  (2022) Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes. Frontiers in Ecology and Evolution 10(): 910009. https://doi.org/10.3389/fevo.2022.910009

2021

• Gurke, Marie; Vidal-Gorosquieta, Amalia; Paijmans, Johanna LA; Wecek, Karolina; Barlow, Axel; Gonzalez-Fortes, Gloria; Hartmann, Stefanie; Grandal-d'Anglade, Aurora; Hofreiter, Michael;  (2021) Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence (vol 16, e0249537, 2021). PLOS ONE 17(6): https://doi.org/10.1371/journal.pone.0249537
• Taron, Ulrike H; Paijmans, Johanna LA; Barlow, Axel; Preick, Michaela; Iyengar, Arati; Drăgușin, Virgil; Vasile, Ștefan; Marciszak, Adrian; Roblíčková, Martina; Hofreiter, Michael; (2021) Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe. Genes 12(2): 144. https://doi.org/10.3390/genes12020144
• Hempel, Elisabeth; Bibi, Faysal; Faith, J Tyler; Brink, James S; Kalthoff, Daniela C; Kamminga, Pepijn; Paijmans, Johanna LA; Westbury, Michael V; Hofreiter, Michael; Zachos, Frank E;  (2021) Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus). Scientific Reports 11(1): 2100. https://doi.org/10.1038/s41598-020-80142-2
• Barlow, Axel; Paijmans, Johanna LA; Alberti, Federica; Gasparyan, Boris; Bar-Oz, Guy; Pinhasi, Ron; Foronova, Irina; Puzachenko, Andrey Y; Pacher, Martina; Dalén, Love; et al (2021) Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Current Biology 31(8): 1771-1779. e7. https://doi.org/10.1016/j.cub.2021.01.073
• Paijmans, Johanna LA; Barlow, Axel; Becker, Matthew S; Cahill, James A; Fickel, Joerns; Förster, Daniel WG; Gries, Katrin; Hartmann, Stefanie; Havmøller, Rasmus Worsøe; Henneberger, Kirstin; et al (2021) African and Asian leopards are highly differentiated at the genomic level. Current Biology 31(9): 1872-1882. e5. https://doi.org/10.1016/j.cub.2021.03.084
• Straube, Nicolas; Lyra, Mariana L; Paijmans, Johanna LA; Preick, Michaela; Basler, Nikolas; Penner, Johannes; Rödel, Mark‐Oliver; Westbury, Michael V; Haddad, Célio FB; Barlow, Axel;  (2021) Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Molecular Ecology Resources 21(7): 2299-2315 https://doi.org/10.1111/1755-0998.13433
• Baleka, Sina; Herridge, Victoria L; Catalano, Giulio; Lister, Adrian M; Dickinson, Marc R; Di Patti, Carolina; Barlow, Axel; Penkman, Kirsty EH; Hofreiter, Michael; Paijmans, Johanna LA;  (2021) Estimating the dwarfing rate of an extinct Sicilian elephant. Current Biology 31(16): 3606-3612. e7. https://doi.org/10.1016/j.cub.2021.05.037
• Taron, Ulrike H; Salado, Isabel; Escobar‐Rodríguez, Mariana; Westbury, Michael V; Butschkau, Susanne; Paijmans, Johanna LA; VonHoldt, Bridgett M; Hofreiter, Michael; Leonard, Jennifer A;  (2021) A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Molecular ecology 30(23): 6340-6354. https://doi.org/10.1111/mec.16037
• Mengüllüoğlu, Deniz; Ambarlı, Hüseyin; Barlow, Axel; Paijmans, Johanna LA; Sayar, Ali Onur; Emir, Hasan; Kandemir, İrfan; Hofer, Heribert; Fickel, Jörns; Förster, Daniel W;  (2021) Mitogenome phylogeny including data from additional subspecies provides new insights into the historical biogeography of the Eurasian lynx Lynx lynx. Genes 12(8): 1216. https://doi.org/10.3390/genes12081216
• Hempel, Elisabeth; Westbury, Michael V; Grau, José H; Trinks, Alexandra; Paijmans, Johanna LA; Kliver, Sergei; Barlow, Axel; Mayer, Frieder; Müller, Johannes; Chen, Lei;  (2021) Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction. Genes 12(8): 1236. https://doi.org/10.3390/genes12081236

2020

• Haruda A, Ventresca Miller AR, Paijmans JLA, Barlow A, Tazhekeyev A, Bilalov S, Hesse Y, Preick M, King T, Thomas R, Härke H, Arzhantseva I (2020) The earliest domestic cat on the Silk Road. Scientific Reports 10: 11241. https://doi.org/10.1038/s41598-020-67798-6
• Paijmans JLA, Barlow A, Henneberger K, Fickel J, Hofreiter M, Foerster DWG (2020) Ancestral mitogenome capture of the Southeast Asian banded linsang. PLoS ONE. 15(6): e0234385. https://doi.org/10.1371/journal.pone.0234385
• Xenikoudakis G, Ahmed M, Harris JC, Wadleigh R, Paijmans JLA, Hartmann S, Barlow A, Lerner H, Hofreiter M (2020) Ancient DNA reveals twenty million years of aquatic life in beavers. Current Biology 30: 110–111. https://doi.org/10.1016/j.cub.2019.12.041
  Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA (2020) Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates. Genes 11: 50. https://doi.org/10.3390/genes11010050

2019

• Sheng GL, Basler N, Ji X-P, Paijmans JLA, Preick M, Hartmann S, Westbury MV, Yuan J-X, Jablonski NG, Alberti F, Xenikoudakis G, Hou X-D, Xiao B, Liu J-H, Hofreiter M, Lai X-L, Barlow A (2019) Palaeogenome reveals genetic contribution of extinct giant panda to extant populations. Current Biology 29: 1695–1700. https://doi.org/10.1016/j.cub.2019.04.021
• Barlow A, Sheng G, Lai, X, Hofreiter M, Pajmans JLA (2019) Once lost, twice found: combined analysis of ancient giant panda sequences further characterises extinct clade. Journal of Biogeography 46: 251–253. https://doi.org/10.1111/jbi.13486
• Signore AV, Paijmans JLA, Hofreiter M, Fago A, Weber RE, Springer MS, Campbell KL (2019) Emergence of a chimeric globin pseudogene and increased hemoglobin oxygen affinity underlie the evolution of aquatic specializations in Sirenia. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msz044
• González-Fortes G, Trucchi TE, Henneberger K, Paijmans JLA, Díez-del Molino D, Schroeder H, Susca R, Barroso-Ruíz C, Bermudez F, Barroso-Medina C, Bettencourt A, Sampaio H, Grandal-d’Anglade A, Salas A, de Lombera A, Fabregas R, Vaquero M, Alonso S, Lozano M, Rodríguez-Alvarez X, Fernández-Rodríguez C, Manica A, Hofreiter M, Barbujani G (2019) A western route of prehistoric human migration from Africa into the Iberian Peninsula. Proceedings of the Royal Society B. https://doi.org/10.1098/rspb.2018.2288
• Sommer RS, Hofreiter M, Krüger F, Siemers BM, Paijmans JLA, Li C, Geige MF (2019) Preliminary results on the molecular study of fish-eating by ‘trawling Myotis’ bat species in Europe. Senckenberg Gesellschaft für Naturforschung. https://doi.org/10.26049/vz69-1-2019-03
• Shapiro B, Barlow A, Heintzman PD, Hofreiter M, Paijmans JLA, Soares AER eds. (2019) Ancient DNA: methods and protocols. Second Edition. New York: Humana Press. https://doi.org/10.1007/978-1-4939-9176-1
• Paijmans JLA, González-Fortes G, Förster D (2019) Application of solid-state capture for the retrieval of small-to-medium sized target loci from ancient DNA. In Ancient DNA: methods and protocols. Second Edition. New York: Humana Press. https://doi.org/10.1007/978-1-4939-9176-1_14
• Henneberger K, Barlow A, Paijmans JLA (2019) Double-stranded library preparation for ancient and other degraded samples. In Ancient DNA: methods and protocols. Second Edition. New York: Humana Press. https://doi.org/10.1007/978-1-4939-9176-1_8
• González-Fortes G, Paijmans JLA (2019) Whole-genome capture of ancient DNA using home-made baits. In Ancient DNA: methods and protocols. Second Edition. New York: Humana Press. https://doi.org/10.1007/978-1-4939-9176-1_11

2018

• Barlow A, Cahill JC, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischauf C, d'Anglade AG, Vázquez AG, Murtskhvaladze M, Saarma U, Anijalg A, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, Hofreiter M (2018) Partial genomic survival of cave bears in living brown bears. Nature Ecology and Evolution 2: 1563–1570. https://doi.org/10.1038/s41559-018-0654-8
• Alberti F, Gonzalez J, Paijmans JLA, Basler N, Preick M, Henneberger K, Trinks A, Rabeder G, Conard NJ, Münzel SC, Joger U, Fritsch G, Hildebrandt T, Hofreiter M, Barlow A (2018) Optimized DNA sampling of ancient bones using Computed Tomography (CT) scans. Molecular Ecology Resources 18: 1196–1208. https://doi.org/10.1111/1755-0998.12911
• Paijmans JLA, Barlow A, Förster DW, Henneberger K, Meyer M, Nickel B, Nagel D, Havmøller RW, Baryshnikov GF, Joger U, Rosendahl W, Hofreiter M (2018) Historical biogeography of the leopard (Panthera pardus) and its extinct European populations. BMC Evolutionary Biology 18: 156. https://doi.org/10.1186/s12862-018-1268-0
• Taron UH, Lell M, Barlow A, Paijmans JLA (2018) Testing of Alignment Parameters for Ancient Samples: Evaluating and optimising mapping parameters for ancient samples using the TAPAS tool. Genes 9, 157. https://doi.org/10.3390/genes9030157

2017

• Paijmans JLA, Barnett R, Reumer JWF, de Vos J, Koot M, Gilbert T, Rohland N, Leonard JA, Barlow A, Hofreiter M (2017) Evolutionary history and extinction dynamics of extinct sabre- and scimitar-toothed cats based on ancient mitogenomes. Current Biology 27, 3330–3336. https://doi.org/10.1016/j.cub.2017.09.033
• Wecek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov B, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Żyła W, Szymura JM, Hofreiter M, Barlow A (2017) Complex admixture preceded and followed the extinction of wisent in the wild. Molecular Biology and Evolution, 34 (3): 598-612. https://doi.org/10.1093/molbev/msw254
• Kehlmaier C, Barlow A (*joint first authors), Hastings AK, Vamberger M, Paijmans JLA, Steadman DW, Albury NA, Franz R, Hofreiter M, Fritz U (2017) Tropical ancient DNA reveals relationships of extinct Bahamian giant tortoise. Proceeding of the Royal Society of London B, 284 (1846), 20162235. https://doi.org/10.1098/rspb.2016.2235
• Westbury M, Baleka S, Barlow A, Hartmann S, Paijmans JLA, Kramarz A, Forasiepi AM, Bond M, Gelfo JN, Reguero MA, Mendoza PL, Taglioretti M, Scaglia F, Rinderknecht A, Jones W, Mena F, Billet G, de Muizon C, Aguilar JL, MacPhee RDE, Hofreiter M. (2017) A mitogenomic timetree for Darwin's enigmatic “transitional” South American mammal, Macrauchenia patachonica. Nature Communications, 8, 15951. https://doi.org/10.1038/ncomms15951
• Gaudry MJ, Jastroch M, Treberg JR, Hofreiter M, Paijmans JLA, Starrett J, Wales N, Signore AV, Springer MS, Campbell KL (2017) Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades. Science Advances 3, e1602878. https://doi.org/10.1126/sciadv.1602878
• Paijmans JLA, Baleka S, Henneberger K, Taron UH, Trinks A, Westbury MV, Barlow A (2017) Sequencing single-stranded libraries on the Illumina NextSeq 500 platform. arXiv 1711.11004. http://arxiv.org/abs/1711.11004

2016

• Paijmans JLA, Fickel J, Courtiol A, Hofreiter M, Förster DW (2016) Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Molecular Ecology Resources 16: 42–55. https://doi.org/10.1111/1755-0998.12420
  Fortes GG, Paijmans JLA (2016) Analysis of whole mitogenomes from ancient samples. In: Whole genome amplification. New York: Humana Press. https://doi.org/10.1007/978-1-4939-2990-0_13

2015

• Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RD, Hofreiter M, Campbell KL (2015) Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Molecular Phylogenetics and Evolution 91: 178–193. https://doi.org/10.1016/j.ympev.2015.05.022

2014

• Hofreiter M, Paijmans JLA, Goodchild H, Speller CF, Barlow A, Fortes GG, Thomas JA, Ludwig A, Collins MJ (2014) The future of ancient DNA: Technical advances and conceptual shifts. BioEssays, 37, 284–293. https://doi.org/10.1002/bies.20140016

2013

• Paijmans JLA, Gilbert MTP, Hofreiter M (2013) Mitogenomic analyses from ancient DNA. Molecular Phylogenetics and Evolution 69: 404–416. https://doi.org/10.1016/j.ympev.2012.06.002
• Zhang H, Paijmans JLA, Chang F, Wu X, Chen G, Lei C, Yang X, Wei Z, Bradley DG, Orlando L, O'Connor T, Hofreiter M (2013) Morphological and genetic evidence for early Holocene cattle management in north-eastern China. Nature Communications 4. https://doi.org/10.1038/ncomms3755
• Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Förster D, Pruvost M, Reissmann M, Bortfeldt R, Adelson DL, Lim SL, Nelson J, Haase B, Engensteiner M, Leeb T, Forsyth G, Mienaltowski MJ, Mahadevan P, Hofreiter M, Paijmans JLA, Gonzalez-Fortes G, Grahn B, Brooks SA. (2013). Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. PLoS ONE 8: e78280. https://doi.org/10.1371/journal.pone.0078280