My research interests have a strong focus on tracing population shifts in response to environmental changes (e.g. climate change), using the palaeogenomic toolkit. Understanding the long-term movement of populations and species under the influence of changing environment is vital to understand how populations adapt (or fail to adapt) to new challenges. I am particularly excited about ancient DNA, as it allows for the investigation of extirpated populations and extinct species: these are essentially cases where the population failed to adapt to an environmental change, and thus of particular importance to study for future conservation of modern populations.

I am willing to supervise a PhD

2024

• PublishedPalaeogenomic data from a Late Pleistocene coprolite clarifies the phylogenetic position of Sicilian cave hyena
  Catalano, G., Iurino, D. A., Modi, A., Paijmans, J., Sardella, R., Sineo, L., Caramelli, D. & Barlow, A., 15 Sept 2024, In: Quaternary Science Reviews. 340, 108859.
  Research output: Contribution to journal › Article › peer-review
• PublishedRecent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx
  Lucena-Perez, M., Paijmans, J., Nocete, F., Nadal, J., Detry, C., Dalén, L., Hofreiter, M., Barlow, A. & Godoy, J., 15 Jan 2024, In: Nature Ecology and Evolution.
  Research output: Contribution to journal › Article › peer-review

2023

• PublishedMuseum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe
  Major, T., Renk, P., Reissig, J., Paijmans, J., Morris, E., Hofreiter, M., Barlow, A., Broadley, D. G. & Wüster, W., 27 Sept 2023, In: PLoS ONE. 18, 9, 19 p., e0291432.
  Research output: Contribution to journal › Article › peer-review

2022

• PublishedTaxonomic Identification of Two Poorly Known Lantern Shark Species Based on Mitochondrial DNA From Wet-Collection Paratypes
  Agne, S., Preick, M., Yang, L., Thiel, R., Weigmann, S., Paijmans, J., Barlow, A., Hofreiter, M. & Straube, N., 30 Jun 2022, In: Frontiers in Ecology and Evolution. 10, 910009.
  Research output: Contribution to journal › Article › peer-review

2021

• PublishedAfrican and Asian leopards are highly differentiated at the genomic level
  Paijmans, J., Barlow, A., Becker, M. S., Cahill, J. A., Fickel, J., Forster, D. W. G., Gries, K., Hartmann, S., Havmoller, R. W., Henneberger, K., Kern, C., Kitchener, A. C., Lorenzen, E. D., Mayer, F., O'Brien, S. J., von Seth, J., Sinding, M.-H. S., Spong, G., Uphyrkina, O., Wachter, B., Westbury, M. V., Dalén, L., Bhak, J., Manica, A. & Hofreiter, M., 10 May 2021, In: Current Biology.
  Research output: Contribution to journal › Article › peer-review
• PublishedAncient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe
  Taron, U. H., Paijmans, J., Barlow, A., Preick, M., Lyengar, A., Dragusin, V., Vasile, S., Marciszak, A., Roblickova, M. & Hofreiter, M., 22 Jan 2021, In: Genes.
  Research output: Contribution to journal › Article › peer-review
• PublishedDiversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction
  Hempel, E., Westbury, M. V., Grau, J. H., Trinks, A., Paijmans, J., Kliver, S., Barlow, A., Mayer, F., Muller, J., Chen, L., Koepfli, K.-P., Hofreiter, M. & Bibi, F., 11 Aug 2021, In: Genes. 12, 8
  Research output: Contribution to journal › Article › peer-review
• PublishedEstimating the dwarfing rate of an extinct Sicilian elephant
  Baleka, S., Herridge, V. L., Catalano, G., Lister, A. M., Dickinson, M. R., Di Patti, C., Barlow, A., Penkman, K., Hofreiter, M. & Paijmans, J., 23 Aug 2021, In: Current Biology.
  Research output: Contribution to journal › Article › peer-review
• E-pub ahead of printIdentifying the true number of specimens of the extinct blue antelope ( Hippotragus leucophaeus )
  Hempel, E., Bibi, F., Faith, J. T., Brink, J. S., Kalthoff, D. C., Kamminga, P., Paijmans, J. L. A., Westbury, M. V., Hofreiter, M. & Zachos, F. E., 22 Jan 2021, (E-pub ahead of print) In: Scientific Reports. 11, 1, 2100.
  Research output: Contribution to journal › Article › peer-review
• PublishedInsight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence
  Gurke, M., Vidal-Gorosquieta, A., Paijmans, J., Wecek, K., Barlow, A., Gonzalez-Fortes, G., Hartmann, S., Grandal-d'Anglade, A. & Hofreiter, M., 28 Apr 2021, In: PLoS ONE.
  Research output: Contribution to journal › Article › peer-review
• PublishedMiddle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears
  Barlow, A., Paijmans, J., Alberti, F., Gasparyan, B., Bar-Oz, G., Pinhasi, R., Foronova, I., Puzachenko, A. Y., Pacher, M., Dalén, L., Baryshnikov, G. & Hofreiter, M., 26 Apr 2021, In: Current Biology.
  Research output: Contribution to journal › Article › peer-review
• PublishedMitogenome phylogeny including data from additional subspecies provides new insights into the historical biogeography of the Eurasian lynx Lynx lynx
  Mengulluoglu, D., Ambarli, H., Barlow, A., Paijmans, J., Sayar, A. O., Emir, H., Kandemir, I., Hofer, H., Fickel, J. & Forster, D. W., 6 Aug 2021, In: Genes. 12, 8
  Research output: Contribution to journal › Article › peer-review
• PublishedSuccessful application of ancient DNA extraction and library construction protocols to museum wet collection specimens
  Straube, N., Lyra, M., Paijmans, J., Preick, M., Basler, N., Penner, J., Rodel, M.-O., Westbury, M. V., Haddad, C. F. B., Barlow, A. & Hofreiter, M., 1 Oct 2021, In: Molecular Ecology Resources.
  Research output: Contribution to journal › Article › peer-review

2020

• PublishedAncestral mitogenome capture of the Southeast Asian banded linsang.
  Paijmans, J., Barlow, A., Henneberger, K., Fickel, J., Hofreiter, M. & Foerster, D. W. G., 30 Jun 2020, In: PLoS ONE.
  Research output: Contribution to journal › Article › peer-review
• PublishedAncient DNA reveals twenty million years of aquatic life in beavers.
  Xenikoudakis, G., Ahmed, M., Harris, J. C., Wadleigh, R., Paijmans, J., Hartmann, S., Barlow, A., Learner, H. & Hofreiter, M., 3 Feb 2020, In: Current Biology. p. 95-111
  Research output: Contribution to journal › Article › peer-review
• PublishedConsensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates.
  Barlow, A., Hartmann, S., Gonzalez, J., Hofreiter, M. & Paijmans, J., 2 Jan 2020, In: Genes. 11, 1
  Research output: Contribution to journal › Article › peer-review
• PublishedThe earliest domestic cat on the Silk Road
  Haruda, A. F., Miller, A. R. V., Paijmans, J., Barlow, A., Tazhekeyev, A., Bailov, S., Hesse, Y., Preick, M., King, T., Thomas, R., Harke, H. & Arzhantseva, L., 9 Jul 2020, In: Scientific Reports.
  Research output: Contribution to journal › Article › peer-review

2019

• PublishedAncient DNA: methods and protocols. Second Edition.
  Shapiro, B. (Editor), Barlow, A. (Editor), Heintzman, P. D. (Editor), Hofreiter, M. (Editor), Paijmans, J. (Editor) & Soares, A. E. (Editor), 16 Mar 2019, Humana New York, NY. (Methods in Molecular Biology)
  Research output: Book/Report › Book
• PublishedApplication of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA
  Paijmans, J. L. A., González Fortes, G. & Förster, D. W., 16 Mar 2019, Ancient DNA. Shapiro, B., Barlow, A., Heintzman, P. D., Hofreiter, M., Paijmans, J. L. A. & Soares, A. E. R. (eds.). New York, NY: Springer New York, Vol. 1963. p. 129-139 11 p.
  Research output: Chapter in Book/Report/Conference proceeding › Chapter
• PublishedDe Sabeltandkat Homotherium Latidens - Een Onderdeel Van De Laat Pleistocene Mammoetfauna Van Het Noordelijk Halfrond
  Reumer, J. W. F., Folkertsma, R. & Paijmans, J., 2019, In: Cranium. 36, 2, p. 5 1 p.
  Research output: Contribution to journal › Article
• PublishedDouble-stranded library preparation for ancient and other degraded samples
  Henneberger, K., Barlow, A. & Paijmans, J., 16 Mar 2019, Ancient DNA: methods and protocols. Second Edition. Humana New York, NY, p. 65-73
  Research output: Chapter in Book/Report/Conference proceeding › Chapter
• PublishedEmergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia
  Signore, A. V., Paijmans, J. L. A., Hofreiter, M., Fago, A., Weber, R. E., Springer, M. S. & Campbell, K. L., 1 Jun 2019, In: Molecular Biology and Evolution. 36, 6, p. 1134-1147
  Research output: Contribution to journal › Article › peer-review
• PublishedPalaeogenome reveals genetic contribution of extinct giant panda to extant populations.
  Sheng, G., Basler, N., Ji, X., Paijmans, J., Alberti, F., Preick, M., Hartmann, S., Westbury, M. V., Yuan, J., Jablonski, N. G., Xenikoudakis, G., Hou, X., Xiao, B., Liu, J.-H., Hofreiter, M., Lai, X. & Barlow, A., 20 May 2019, In: Current Biology. 29, 10, p. 1695-1700
  Research output: Contribution to journal › Article › peer-review
• PublishedPreliminary results on the molecular study of fish-eating by ‘trawling Myotis’ bat species in Europe
  Sommer, R. S., Hofreiter, M., Krüger, F., Siemers, B. M., Paijmans, J. L. A., Li, C. & Geiger, M. F., 27 Feb 2019, In: Vertebrate Zoology.
  Research output: Contribution to journal › Article › peer-review
• PublishedWhole-Genome Capture of Ancient DNA Using Homemade Baits
  Fortes, G. & Paijmans, J. L. A., 2019, Methods in Molecular Biology (Clifton, N.J.). Vol. 1963. p. 93-105 13 p.
  Research output: Chapter in Book/Report/Conference proceeding › Chapter

2018

• PublishedHistorical biogeography of the leopard (Panthera pardus) and its extinct European populations.
  Paijmans, J., Barlow, A., Forster, D. W., Henneberger, K., Meyer, M., Nickel, B., Nagel, D., Havmoller, R. W., Baryshnikov, G., Joger, U., Rosendahl, W. & Hofreiter, M., 23 Oct 2018, In: BMC Evolutionary Biology. 18, 156.
  Research output: Contribution to journal › Article › peer-review
• PublishedOptimized DNA sampling of ancient bones using Computed Tomography scans
  Alberti, F., Gonzalez, J., Paijmans, J. L. A., Basler, N., Preick, M., Henneberger, K., Trinks, A., Rabeder, G., Conard, N. J., Münzel, S. C., Joger, U., Fritsch, G., Hildebrandt, T., Hofreiter, M. & Barlow, A., 1 Nov 2018, In: Molecular Ecology Resources. 18, 6, p. 1196-1208 13 p.
  Research output: Contribution to journal › Article › peer-review
• PublishedPartial genomic survival of cave bears in living brown bears.
  Barlow, A., Cahill, J. A., Hartmann, S., Theunert, C., Xenikoudakis, G., Fortes, G. G., Paijmans, J., Rabeder, G., Frischauf, C., Grandal-d'Anglade, A., García-Vázquez, A., Murtskhvaladze, M., Saarma, U., Anijalg, P., Skrbinšek, T., Bertorelle, G., Gasparian, B., Bar-Oz, G., Pinhasi, R., Slatkin, M., Dalén, L., Shapiro, B. & Hofreiter, M., 27 Aug 2018, In: Nature Ecology and Evolution. 2, p. pages 1563–1570
  Research output: Contribution to journal › Article › peer-review
• PublishedTargeted resequencing of coding DNA sequences for SNP discovery in nonmodel species
  Förster, D. W., Bull, J. K., Lenz, D., Autenrieth, M., Paijmans, J. L. A., Kraus, R. H. S., Nowak, C., Bayerl, H., Kuehn, R., Saveljev, A. P., Sindičić, M., Hofreiter, M., Schmidt, K. & Fickel, J., 1 Nov 2018, In: Molecular Ecology Resources. 18, 6, p. 1356-1373 18 p.
  Research output: Contribution to journal › Article › peer-review
• PublishedTesting of Alignment Parameters for Ancient Samples: Evaluating and optimising mapping parameters for ancient samples using the TAPAS tool.
  Taron, U. H., Lell, M., Barlow, A. & Paijmans, J., 13 Mar 2018, In: Genes. 9, 3, 157.
  Research output: Contribution to journal › Article › peer-review

2017

• PublishedA mitogenomic timetree for Darwin’s enigmatic “transitional” South American mammal, Macrauchenia patachonica.
  Westbury, M. V., Baleka, S., Barlow, A., Hartmann, S., Paijmans, J., Forasiepi, A. M., Kramarz, A., Bond, M., Gelfo, J. N., Gelfo, J. N., Reguero, M. A., Lopez-Mendoza, P., Taglioretti, M., Scaglia, F., Rinderknecht, A., Jones, W., Mena, F., Billet, G., de Muizon, C., Aguilar, J. L., Mac Phee, R. D. E. & Hofreiter, M., 27 Jul 2017, In: Nature Communications. 15951.
  Research output: Contribution to journal › Article › peer-review
• PublishedComplex admixture preceded and followed the extinction of wisent in the wild.
  Wecek, K., Hartmann, S., Paijmans, J., Taron, U. H., Xenikoudakis, G., Cahill, J. A., Heintzman, P. D., Shapiro, B., Baryshnikov, G., Bunevich, A. N., Crees, J. J., Dobosz, R., Manaserian, N., Okarma, H., Tokarska, M., Turvey, S., Wojcik, J. M., Zyla, W., Szymura, J. M., Hofreiter, M. & Barlow, A., 1 Mar 2017, In: Molecular Biology and Evolution. 34, 7, p. 598-612
  Research output: Contribution to journal › Article › peer-review
• PublishedEvolutionary history and extinction dynamics of extinct sabre- and scimitar-toothed cats based on ancient mitogenomes.
  Paijmans, J., Barnett, R., Gilbert, M. T. P., Zepeda-Mendoza, M. L., Reumer, J. W. F., de Vos, J., Zazula, G., Nagel, D., Baryshnikov, G., Leonard, J. A., Rohland, N., Westbury, M. V., Barlow, A. & Hofreiter, M., 6 Nov 2017, In: Current Biology.
  Research output: Contribution to journal › Article › peer-review
• PublishedInactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades
  Gaudry, M. J., Jastroch, M., Treberg, J. R., Hofreiter, M., Paijmans, J. L. A., Starrett, J., Wales, N., Signore, A. V., Springer, M. S. & Campbell, K. L., 7 Jul 2017, In: Science Advances. 3, 7, p. e1602878
  Research output: Contribution to journal › Article › peer-review
• PublishedSequencing single-stranded libraries on the Illumina NextSeq 500 platform.
  Paijmans, J., Baleka, S., Henneberger, K., Taron, U. H., Trinks, A., Westbury, M. V. & Barlow, A., 29 Nov 2017.
  Research output: Working paper › Preprint
• PublishedTropical ancient DNA reveals relationships of extinct Bahamian giant tortoise.
  Kehlmaier, C., Barlow, A., Hastings, A. K., Vamberger, M., Paijmans, J., Steadman, D., Albury, N. A., Franz, R., Hofreiter, M. & Fritz, U., 11 Jan 2017, In: Proceedings of the Royal Society B: Biological Sciences. 284, 1846
  Research output: Contribution to journal › Article › peer-review

2016

• PublishedAnalysis of whole mitogenomes from ancient samples
  Fortes, G. G. & Paijmans, J. L. A., 2016, Whole genome amplification. Kroneis, T. (ed.). Humana Press, USA, (Methods in Molecular Biology).
  Research output: Chapter in Book/Report/Conference proceeding › Chapter
• PublishedImpact of enrichment conditions on cross-species capture of fresh and degraded DNA
  Paijmans, J. L. A., Fickel, J., Courtiol, A., Hofreiter, M. & Förster, D. W., 1 Jan 2016, In: Molecular Ecology Resources. 16, 1, p. 42-55 14 p.
  Research output: Contribution to journal › Article › peer-review
• PublishedMassive influence of DNA isolation and library preparation approaches on palaeogenomic sequencing data
  Barlow, A., Fortes, G. M. G., Dalen, L., Pinhasi, R., Gasparyan, B., Rabeder, G., Frischauf, C., Paijmans, J. L. A. & Hofreiter, M., 1 Sept 2016, In: bioRxiv. p. 075911 1 p.
  Research output: Contribution to journal › Article

2015

• PublishedInterordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia
  Springer, M. S., Signore, A. V., Paijmans, J. L. A., Vélez-Juarbe, J., Domning, D. P., Bauer, C. E., He, K., Crerar, L., Campos, P. F., Murphy, W. J., Meredith, R. W., Gatesy, J., Willerslev, E., MacPhee, R. D. E., Hofreiter, M. & Campbell, K. L., 1 Oct 2015, In: Molecular Phylogenetics and Evolution. 91, p. 178-193 16 p.
  Research output: Contribution to journal › Article › peer-review
• PublishedThe future of ancient DNA: Technical advances and conceptual shifts.
  Hofreiter, M., Paijmans, J., Goodchild, H., Speller, C. F., Barlow, A., Fortes, G. G., Thomas, J. A., Ludwig, A. & Collins, M. J., 1 Mar 2015, In: BioEssays. 37, p. 284-293
  Research output: Contribution to journal › Article › peer-review

2013

• PublishedEvidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse
  Bellone, R. R., Holl, H., Setaluri, V., Devi, S., Maddodi, N., Archer, S., Sandmeyer, L., Ludwig, A., Foerster, D., Pruvost, M., Reissmann, M., Bortfeldt, R., Adelson, D. L., Lim, S. L., Nelson, J., Haase, B., Engensteiner, M., Leeb, T., Forsyth, G., Mienaltowski, M. J., Mahadevan, P., Hofreiter, M., Paijmans, J. L. A., Gonzalez-Fortes, G., Grahn, B. & Brooks, S. A., 22 Oct 2013, In: PLoS ONE. 8, 10, p. e78280
  Research output: Contribution to journal › Article › peer-review
• PublishedMitogenomic analyses from ancient DNA
  Paijmans, J. L. A., Gilbert, M. T. P. & Hofreiter, M., 1 Nov 2013, In: Molecular Phylogenetics and Evolution. 69, p. 404-416 13 p.
  Research output: Contribution to journal › Article › peer-review
• PublishedMorphological and genetic evidence for early Holocene cattle management in northeastern China
  Zhang, H., Paijmans, J. L. A., Chang, F., Wu, X., Chen, G., Lei, C., Yang, X., Wei, Z., Bradley, D. G., Orlando, L., O’Connor, T. & Hofreiter, M., 8 Nov 2013, In: Nature Communications. 4, 2755.
  Research output: Contribution to journal › Article › peer-review

2012

• PublishedClovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves
  Jenkins, D. L., Davis, L. G., Stafford, T. W., Campos, P. F., Hockett, B., Jones, G. T., Cummings, L. S., Yost, C., Connolly, T. J., Yohe, R. M., Gibbons, S. C., Raghavan, M., Rasmussen, M., Paijmans, J. L. A., Hofreiter, M., Kemp, B. M., Barta, J. L., Monroe, C., Gilbert, M. T. P. & Willerslev, E., 13 Jul 2012, In: Science. 337, 6091, p. 223-228 6 p.
  Research output: Contribution to journal › Article › peer-review