Publications

Here is the full list of publications from group members. You can also check out the personal webpages for individual publications

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

Lyra ML, Lourenço ACC, Pinheiro PDP, Pezzuti TL, Baêta D, Barlow A, Hofreiter M, Pombal José PJR, Haddad CFB, Faivovich J (2020) High-throughput DNA sequencing of museum specimens sheds light on the long-missing species of the Bokermannohyla claresignata group (Anura: Hylidae: Cophomantini). Zoological Journal of the Linnean Society. https://doi.org/10.1093/zoolinnean/zlaa033

Naito YI, Meleg IN, Robu M, Vlaicu M, Drucker DG, Wißing C, Hofreiter M, Barlow A, Bocherens H (2020) Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis. Scientific Reports 10: 6612. https://doi.org/10.1038/s41598-020-62990-0

Westbury MV, Hartmann S, Barlow A, Preick M, Ridush B, Nagel D, Rathgeber T, Ziegler R, Baryshnikov G, Sheng G, Ludwig A, Wiesel I, Dalen L, Bibi F, Werdelin L, Heller R, Hofreiter M (2020) Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena. Science Advances 6 (11): eaay0456. https://doi.org/10.1126/sciadv.aay0456

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

Barlow A, Hofreiter M, Knapp M (2019) Cave bears and ancient DNA: a mutually beneficial relationship. In Berichte der Geologischen Bundesanstalt Nr. 132. Festschrift zum 80. Geburtstag von emer. Univ.-Prof. Dr. Mag. Gernot Rabeder. ISSN: 1017-8880

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

Barlow A, Wüster W, Kelly CMR, Branch WR, Phelps T, Tolley KA (2019) Ancient habitat shifts and organismal diversification are decoupled in the African viper genus Bitis (Serpentes: Viperidae). Journal of Biogeography 46: 1234–1248. https://doi.org/10.1111/jbi.13578

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

Yuan J-X, Hou X-D, Barlow A, Preick M, Taron U, Alberti F, Basler N, Deng T, Lai X-L, Hofreiter M, Sheng G-L (2019) Molecular identification of Late and terminal Pleistocene Equus ovodovi from northeastern China. PLoS ONE 14: e0216883. https://doi.org/10.1371/journal.pone.0216883

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

Westbury MV, Hartmann S, Barlow A, Wiesel I, Leo V, Welch R, Parker DM, Sicks F, Ludwig A, Dalén L, Hofreiter M (2018) Extended and continuous decline in effective population size results in low genomic diversity but no signs of inbreeding in the world’s rarest hyena species, the brown hyena. Molecular Biology and Evolution 35: 1225–1237. https://doi.org/10.1093/molbev/msy037

Wüster W, Chirio L, Trape J-F, Ineich I, Jackson K, Greenbaum E, Barron C, Kusamba C, Nagy ZT, Storey R, Hall C, Wüster CE, Barlow A, Broadley DG (2018) Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae). Zootaxa 4455: 68–98. http://dx.doi.org/10.11646/zootaxa.4455.1.3

Thorpe R, Barlow A, Surget-Groba Y, Malhotra A (2018) Multilocus phylogeny, species age and biogeography of the Lesser Antillean anoles. Molecular Phylogenetics and Evolution 127: 682–695. https://doi.org/10.1016/j.ympev.2018.06.014

Sheng G-L, Barlow A, Cooper A, Hou X-D, Ji X-P, Jablonski NG, Zhong B-J, Liu H, Flynn LJ, Yuan J-X, Wang L-R, Basler N, Hofreiter M, Lai XL (2018) Ancient DNA from giant panda (Ailuropoda melanoleuca) of Southwestern China reveals genetic diversity loss during the Holocene. Genes 9: 198. https://doi.org/10.3390/genes9040198

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

Basler N, Xenikoudakis G, Westbury MV, Song L, Sheng G, Barlow A (2017) Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone. BMC Research Notes 10, 754. https://doi.org/10.1186/s13104-017-3061-3

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

Beck SV, Carvalho GR, Barlow A, Rüber L, Tan HH, Nugroho E, Wowor D, Azizah MNS, Herder F, Muchlisin ZA, de Bruyn M (2017) Plio-Pleistocene phylogeography of the Southeast Asian blue panchax killifish, Aplocheilus panchax. PLoS ONE, 12: e0179557. https://doi.org/10.1371/journal.pone.0179557

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

Fortes GG, Grandal-d’Anglade A, Kolbe B, Fernandes D, Meleg IN, García-Vázquez A, Pinto-Llona AC, Constantin S, de Torres TJ, Ortiz JE, Frischauf C, Rabeder G, Hofreiter M, Barlow A (2016) Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Molecular Ecology, 25, 4907–4918. https://doi.org/10.1111/mec.13800

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

Maddock ST, Childerstone A, Fry BG, Williams DJ, Barlow A, Wüster W (2016) Multi-locus phylogeny and species delimitation of Australo-Papuan blacksnakes (Pseudechis Wagler, 1830: Elapidae: Serpentes). Molecular Phylogenetics and Evolution, 107, 48–55. https://doi.org/10.1016/j.ympev.2016.09.005

Zancolli G, Baker T, Barlow A, Bradley RK, Calvete JJ, Carter KC, de Jager K, 1, Owens JB, Price JF, Sanz L, Scholes-Higham A, Shier L, Wood L, Wüster CE, Wüster W (2016) Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus × viridis Hybrid Zone in Southwestern New Mexico. Toxins, 8, 188. https://doi.org/10.3390/toxins8060188

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

Thorpe RS, Barlow A, Malhotra A, Surget-Groba Y (2015) Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change. Molecular Ecology, 24, 1019–30. https://doi.org/10.1111/mec.13093

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.201400160

2013

Barlow A, Baker K, Hendry CR, Peppin L, Phelps T, Tolley KA, Wüster CE, Wüster W (2013) Phylogeography of the widespread African puff adder (Bitis arietans) reveals multiple Pleistocene refugia in southern Africa. Molecular Ecology, 22, 1134–57. https://doi.org/10.1111/mec.12157

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

2012

Barlow A, Grail W, de Bruyn M, Wüster W (2012) Anonymous nuclear markers for the African adders (Serpentes: Viperidae: Bitis). Conservation Genetics Resources, 4, 967–969. https://doi.org/10.1007/s12686-012-9684-8

Jenkins DL, Davis LG, Stafford TW Jr, Campos PF, Hockett B, Jones GT, Cummings LS, Yost C, Connolly TJ, Yohe RM, Gibbons SC, Raghavan M, Rasmussen M, Paijmans JLA, Hofreiter M, Kemp BM, Barta JL, Monroe C, Gilbert MTP, Willerslev E (2012) Clovis age western stemmed projectile points and human coprolites at the paisley caves. Science 337: 223–228. https://doi.org/10.1126/science.1218443

Richards DP, Barlow A, Wüster W (2012) Venom lethality and diet: Differential responses of natural prey and model organisms to the venom of the saw-scaled vipers (Echis). Toxicon, 59, 110–116. https://doi.org/10.1016/j.toxicon.2011.10.015

2010

de Bruyn M, Grail W, Barlow A, Carvalho GR (2010) Anonymous nuclear markers for SouthEast Asian halfbeak fishes (Dermogenys). Conservation Genetics Resources, 2, 325–327. https://doi.org/10.1007/s12686-010-9228-z

2009

Barlow A, Pook CE, Harrison R, Wüster W (2009) Coevolution of diet and prey-specific venom activity supports the role of selection in snake venom evolution. Proceedings of The Royal Society B, 276, 2443–2449. https://doi.org/10.1098/rspb.2009.0048


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