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Group Publications (2014-2018)

2018

  • Barlow, A., Cahill, J.A., Hartmann, S., Theunert, C., Xenikoudakis, G., Fortes, G.G., Paijmans, J.L.A., 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. and Hofreiter, M. (2018) Partial genomic survival of cave bears in living brown bears. Nature Ecology and Evolution, DOI: 10.1038/s41559-018-0654-8.
  • 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. and Barlow, A. (2018)Optimized DNA sampling of ancient bones using Computed Tomography scans. Mol Ecol Resour, published online 7th June 2018, doi: 10.1111/1755-0998.12911.
  • Beermann, J., Westbury, M.V., Hofreiter, M., Hilgers, L., Deister, F., Neumann, H. and Raupach, M.J. (2018) Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep, 8 (1), 6893 (doi: 10.1038/s41598-018-25225-x).
  • Grau, J.H., Hackl, T., Koepfli, K.P. and Hofreiter, M. (2018) Improving draft genome contiguity with reference-derived in silico mate-pair libraries. Gigascience, 7 (5) (published online 21st April 2018, doi: 10.1093/gigascience/giy029).
  • Wutke, S., Sandoval-Castellanos, E., Benecke, N., Döhle, H.J., Friederich, S., Gonzalez, J., Hofreiter, M., Lõugas, L., Magnell, O., Malaspinas, A.S., Morales-Muñiz, A., Orlando, L., Reissmann, M., Trinks, A. and Ludwig, A. (2018) Decline of genetic diversity in ancient domestic stallions in Europe. Sci Adv 4 (4), eaap9691 (published online 18th April 2018, doi: 10.1126/sciadv.aap9691, eCollection 2018 April).
  • Hilgers, L., Hartmann, S., Hofreiter, M. and von Rintelen, T. (2018) Novel genes, ancient genes, and gene co-option contributed to the genetic basis of the radula, a molluscan innovation. Mol Biol Evol, 35 (7), 1638-1652 (published online 17th April 2018. doi: 10.1093/molbev/msy052).
  • Sheng, G.L., Barlow, A., Cooper, A., Hou, X.D., Ji, X.P., Jablonski, N.G., Zhong, B.J., Liu, H., Flynn, L.J., Yuan, J.X., Wang, L.R., Basler, N., Westbury, M.V., Hofreiter, M. and Lai, X.L. (2018) Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene. Genes (Basel), 9 (4), E198 (doi: 10.3390/genes9040198).
  • Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour. 2018;00:1–13. doi:10.1111/1755-0998.12932
  • Westbury, M.V., Hartmann, S., Barlow, A., Wiesel, I., Leo, V., Welch, R., Parker, D.M., Sicks, F., Ludwig, A., Dalén, L. and Hofreiter, M. (2018) Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena. Mol Biol Evol, published online 8th March 2018 doi: 10.1093/molbev/msy037.
  • Palkopoulou, E., Lipson, M., Mallick, S., Nielsen, S., Rohland, N., Baleka, S., Karpinski, E., Ivancevic, A.M., To, T.H., Kortschak, R.D., Raison, J.M., Qu, Z., Chin, T.J., Alt, K.W., Claesson, S., Dalén, L., MacPhee, R.D.E., Meller, H., Roca, A.L., Ryder, O.A., Heiman, D., Young, S., Breen, M., Williams, C., Aken, B.L., Ruffier, M., Karlsson, E., Johnson, J., Di Palma, F., Alfoldi, J., Adelson, D.L., Mailund, T., Munch, K., Lindblad-Toh, K., Hofreiter, M., Poinar, H. and Reich, D. (2018) A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci USA 115 (11), E2566-E2574 (published online 26th February 2018 doi: 10.1073/pnas.1720554115).
  • Gaunitz, C., Fages, A., Hanghøj, K., Albrechtsen, A., Khan, N., Schubert, M., Seguin-Orlando, A., Owens, I.J., Felkel, S., Bignon-Lau, O., de Barros Damgaard, P., Mittnik, A., Mohaseb, A.F., Davoudi, H., Alquraishi, S., Alfarhan, A.H., Al-Rasheid, K.A.S., Crubézy, E., Benecke, N., Olsen, S., Brown, D., Anthony, D., Massy, K., Pitulko, V., Kasparov, A., Brem, G., Hofreiter, M., Mukhtarova, G., Baimukhanov, N., Lõugas, L., Onar, V., Stockhammer, P.W., Krause, J., Boldgiv, B., Undrakhbold, S., Erdenebaatar, D., Lepetz, S., Mashkour, M., Ludwig, A., Wallner, B., Merz, V., Merz, I., Zaibert, V., Willerslev, E., Librado, P., Outram, A.K. and Orlando, L. (2018) Ancient genomes revisit the ancestry of domestic and Przewalski's horses. Science, published online 22nd February 2018 (doi: 10.1126/science.aao3297).

2017

  • Paijmans, J.L.A., Barnett, R., Gilbert, M.T.P., Zepeda-Mendoza, M.L., Reumer, J.W.F., de Vos, J., Zazula, G., Nagel, D., Baryshnikov, G.F., Leonard, J.A., Rohland, N., Westbury, M.V., Barlow, A. and Hofreiter, M. (2017) Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics. Curr Biol 27 (21), 3330-3336.e5. (published online 19th October 2017, doi: 10.1016/j.cub.2017.09.033.).
  • Casas-Marce, M., Marmesat, E., Soriano, L., Martínez-Cruz, B., Lucena, M., Nocete, F., Rodríguez-Hidalgo, A., Canals, A., Nadal, J., Detry, C., Bernáldez-Sánchez, E., Fernández-Rodríguez, C., Pérez-Ripoll, M., Stiller, M., Hofreiter, M., Rodríguez, A., Revilla, E., Delibes, M. and Godoy, J.A. (2017) Spatio-temporal dynamics of genetic variation in the Iberian lynx along its path to extinction reconstructed with ancient DNA. Mol Biol Evol 34 (11), 2893-2907 (published online 29th August 2017, doi: 10.1093/molbev/msx222).
  • Claesson, S., Baleka, S., Hofreiter, M. and  Widga, C. (2017)  The contribution of Late Pleistocene megafauna finds to submerged archaeology and the interpretation of ancient coastal landscapes. Journal of Archaeological Science: Reports 15, 290-298.
  • Xiang, H., Gao, J., Cai, D., Luo, Y., Yu, B., Liu, L., Liu, R., Zhou, H., Chen, X., Dun, W., Wang, X., Hofreiter, M. and Zhao X. (2017) Origin and dispersal of early domestic pigs in northern China. Sci Rep 7 (1), 5602 (published online 10th August 2017, doi: 10.1038/s41598-017-06056-8.
  • Gaudry, M.J., Jastroch, M., Treberg, J.R., Hofreiter, M., Paijmans, J.L.A., Starrett, J., Wales, N., Signore, A.V., Springer, M.S. and Campbell, K.L. (2017) Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades. Science Advances, 3 (7), e1602878 (published online 12th July 2017, doi: 10.1126/sciadv.1602878).
  • Westbury, M. Baleka, S., Barlow, A., Hartmann, S., Paijmans, J.L.A., Kramarz, A., Forasiepi, A.M., Bond, M., Gelfo, J.N., Reguero, M.A., Mendoza, P.L., Taglioretti, M., Scaglia, F., Rinderknecht, A., Jones, W., Mena, F., Billet, G., de Muizon, C., Aguilar, J.L., MacPhee, R.D.E. and Hofreiter, M. (2017) A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica. Nature Communications, 8, 15951 (published online 17th June 2017, doi: 10.1038/ncomms15951).
  • Thomas, J.E., Carvalho, G.R., Haile, J., Martin, M.D., Castruita, J.A.S., Niemann, J., Sinding, M.S., Sandoval-Velasco, M., Rawlence, N.J., Fuller, E., Fjeldså, J., Hofreiter, M., Stewart, J.R., Gilbert, M.T.P. and Knapp, M. (2017) An ‛Aukward' Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks. Genes (Basel), 8 (6), E164 (published online 15th June 2017, doi: 10.3390/genes8060164).
  • Westbury, M., Dalerum, F., Norén, K. and Hofreiter, M. (2017) Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations, Mitochondrial DNA Part B, 2 (1), 298-299 (DOI: 10.1080/23802359.2017.1331325).
  • Meyer, M., Palkopoulou, E., Baleka, S., Stiller, M., Penkman, K.E.H., Alt, K.W., Ishida, Y., Mania, D., Mallick, S., Meijer, T., Meller, H., Nagel, S., Nickel, B., Ostritz, S., Rohland, N., Schauer, K., Schüler, T., Roca, A.L., Reich, D., Shapiro, B. and Hofreiter, M. (2017) Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. Elife, 6, e25413 (published online 6th June 2017, doi: 10.7554/eLife.25413).
  • González-Fortes, G., Jones, E.R., Lightfoot, E., Bonsall, C., Lazar, C., Grandal-d'Anglade, A., Garralda, M.D., Drak, L., Siska, V., Simalcsik, A., Boroneanţ, A., Vidal Romaní, J.R., Vaqueiro Rodríguez, M., Arias, P., Pinhasi, R., Manica, A. and Hofreiter, M. (2017) Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin. Curr Biol, 27 (12), 1801-1810 (published online 24th May 2017, doi: 10.1016/j.cub.2017.05.023).
  • Elsner, J., Hofreiter, M., Schibler, J. and Schlumbaum, A. (2017) Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum. PLoS One, 12 (5), e0177458 (published online 24th May 2017, doi: 10.1371/journal.pone.0177458).
  • Librado, P., Gamba, C., Gaunitz, C., Der Sarkissian, C., Pruvost, M., Albrechtsen, A., Fages, A., Khan, N., Schubert, M., Jagannathan, V., Serres-Armero, A., Kuderna, L.F.K., Povolotskaya, I.S., Seguin-Orlando, A., Lepetz, S., Neuditschko, M., Thèves, C., Alquraishi, S., Alfarhan, A.H., Al-Rasheid, K., Rieder, S., Samashev, Z., Francfort, H.P., Benecke, N., Hofreiter, M., Ludwig, A., Keyser, C., Marques-Bonet, T., Ludes, B., Crubézy, E., Leeb, T., Willerslev, E. and Orlando, L. (2017) Ancient genomic changes associated with domestication of the horse. Science, 356 (6336), 442-445 (published online 28th April 2017, doi: 10.1126/science.aam5298).
  • Dolotovskaya, S., Bordallo, J.T., Haus, T., Noll, A., Hofreiter, M., Zinner, D. and Roos, C. (2017) Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio). Zool J Linn Soc, 181 (2), 471-483 (published online 27th April 2017, doi: 10.1093/zoolinnean/zlx001).
  • Chang, D., Knapp, M., Enk, J., Lippold, S., Kircher, M., Lister, A., MacPhee, R.D., Widga, C., Czechowski, P., Sommer, R., Hodges, E., Stümpel, N., Barnes, I., Dalén, L., Derevianko, A., Germonpré, M., Hillebrand-Voiculescu, A., Constantin, S., Kuznetsova, T., Mol, D., Rathgeber, T., Rosendahl, W., Tikhonov, A.N., Willerslev, E., Hannon, G., Lalueza-Fox, C., Joger, U., Poinar, H., Hofreiter, M. and Shapiro, B. (2017) The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci Rep, 7, 44585 (published online 22nd March 2017, doi: 10.1038/srep44585).
  • Siska, V., Jones, E.R., Jeon, S., Bhak, Y., Kim, H., Cho, Y.S., Kim, H., Lee, K., E. Veselovskaya5, E., T. Balueva, T., Gallego-Llorente, M., Hofreiter, M., Bradley, D. G., Eriksson, A., Pinhasi, R., Bhak, J. and Manica, A. (2016) Genome-wide data from two early Neolithic East Asian individuals dating to 7,700 years ago. Science Advances, 3 (2), e1601877 (published online 1st Feb 2017, doi: 10.1126/sciadv.1601877).
  • Kehlmaier, C., Barlow, A., Hastings, A.K., Vamberger, M., Paijmans, J.L., Steadman, D.W., Albury, N.A., Franz, R., Hofreiter, M. and Fritz, U. (2017) Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum. Proc Biol Sci, 284 (1846), 20162235 (doi: 10.1098/rspb.2016.2235).

2016

  • Fortes, G.G., Grandal-d'Anglade, A., Kolbe, B., Fernandes, D., Meleg, I.N., García-Vázquez, A., Pinto-Llona, A.C., Constantin, S., de Torres, T.J., Ortiz, J.E., Frischauf, C., Rabeder, G., Hofreiter, M and Barlow, A. (2016) Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Molecular Ecology, 25 (19), 4907-4918 (published online 10th August 2016, doi: 10.1111/mec.13800).
  • Wutke, S., Andersson, L., Benecke, N., Sandoval-Castellanos, E., Gonzalez, J., Hallsson, J.H., Lõugas, L., Magnell, O., Morales-Muniz, A., Orlando, L., Pálsdóttir, A.H., Reissmann, M., Muñoz-Rodríguez, M.B., Ruttkay, M., Trinks, A., Hofreiter, M. and Ludwig A. (2016) The origin of ambling horses. Current Biology, 26 (15), R697-9 (published online 8th August 2016, doi: 10.1016/j.cub.2016.07.001).
  • Gallego-Llorente, M., Connell, S., Jones, E.R., Merrett, D.C., Jeon, Y., Eriksson, A., Siska, V., Gamba, C., Meiklejohn, C., Beyer, R., Jeon, S., Cho, Y.S., Hofreiter, M., Bhak, J., Manica, A. and Pinhasi R. (2016) The genetics of an early Neolithic pastoralist from the Zagros, Iran. Scientific Reports, 6, 31,326, published online 9th August 2016, doi: 10.1038/srep31326.
  • Speller, C., van den Hurk, Y., Charpentier, A., Rodrigues, A., Gardeisen, A., Wilkens, B., McGrath, K., Rowsell, K., Spindler, L., Collins, M. and Hofreiter M. (2016) Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans. Philos Trans R Soc Lond B Biol Sci., 371 (1702), pii: 20150332 (doi: 10.1098/rstb.2015.0332).
  • Elsner, J., Deschler-Erb, S., Stopp, B., Hofreiter, M., Schibler, J. and Schlumbaum, A. (2016) Mitochondrial d-loop variation, coat colour and sex identification of Late Iron Age horses in Switzerland. Journal of Archaeological Science: Reports 6, 386–396 (doi: dx.doi.org/10.1016/j.jasrep.2016.03.007).
  • Mohandesan, E., Speller, C.F., Peters, J., Uerpmann, H.P., Uerpmann, M., De Cupere, B., Hofreiter, M. and Burger, P.A. (2016) Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel. Molecular Ecology Resources, 17 (2), 300-313. (published online 11th June 2016, doi: 10.1111/1755-0998.12551).
  • Hilgers, L., Grau, J. H., Pfaender, J., & von Rintelen, T. (2016). The complete mitochondrial genome of the viviparous freshwater snail Tylomelania sarasinorum (Caenogastropoda: Cerithioidea). Mitochondrial DNA Part B, 1 (1), 330-331 (doi: 10.1080/23802359.2016.1172046).
  • Almathen, F., Charruau, P., Mohandesan, E., Mwacharo, J.M., Orozco-terWengel, P., Pitt, D., Abdussamad, A.M., Uerpmann, M., Uerpmann, H.P., De Cupere, B., Magee, P., Alnaqeeb, M.A., Salim, B., Raziq, A., Dessie, T., Abdelhadi, O.M., Banabazi, M.H., Al-Eknah, M., Walzer, C., Faye, B., Hofreiter, M., Peters, J., Hanotte, O., Burger, P.A. (2016) Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary. Proc Natl Acad Sci USA, 113 (24), 6707-6712 (published online 9th May 2016, doi: 10.1073/pnas.1519508113).
  • Rainford, J.L., Hofreiter, M. and Mayhew, P.J. (2016) Phylogenetic analyses suggest that diversification and body size evolution are independent in insects. BMC Evol Biol, 16, 8 (doi: 10.1186/s12862-015-0570-3).

2015

  • Jones, E.R., Gonzalez-Fortes, G., Connell, S., Siska, V., Eriksson, A., Martiniano, R., McLaughlin, R.L., Gallego-Llorente, M., Cassidy, L.M., Gamba, C., Meshveliani, T., Bar-Yosef, O., Müller, W., Belfer-Cohen, A., Matskevich, Z., Jakeli, N., Higham, T.F., Currat, M., Lordkipanidze, D., Hofreiter, M., Manica, A., Pinhasi, R. and Bradley, D.G. (2016) Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat Commun 6, 8912 (doi: 10.1038/ncomms9912).
  • Gallego-Llorente, M., Jones, E.R., Eriksson, A., Siska, V., Arthur, K.W., Arthur, J.W., Curtis, M.C., Stock, J.T., Coltorti, M., Pieruccini, P., Stretton, S., Brock, F., Higham, T., Park, Y., Hofreiter, M., Bradley, D.G., Bhak, J., Pinhasi, R. and Manica, A. (2015) Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350 (6262), 820-822 (published online 8th Oct 2015; doi: 10.1126/science.aad2879).
  • Li, C., Corrigan, S., Yang, L., Straube, N., Harris, M., Hofreiter, M., White, W. and Naylor, G.J.P. (2015) DNA capture reveals transoceanic gene flow in endangered river sharks. Proc. Natl. Acad. Sci. U S A, 112 (43), 13,302-13,307 (published online 12th Oct 2015¸ doi: 10.1073/pnas.1508735112).
  • Hartmann, S., Hasenkamp, N., Mayer, J., Michaux, J., Morand, S., Mazzoni, C.J., Roca, A.L and Greenwood, A.D. (2015) Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse. BMC Genomics, 16, 613 (published online 18th August 2015, doi: 10.1186/s12864-015-1766-z).
  • Campbell, K.L. and Hofreiter, M. (2015) Resurrecting phenotypes from ancient DNA sequences: promises and perspectives. Canadian Journal of Zoology, 93 (9), 701-710 (published online 24th July 2015, doi: 10.1139/cjz-2014-0337).
  • Le Duc, D., Renaud, G., Krishnan, A., Almén, M.S., Huynen, L., Prohaska, S.J., Ongyerth, M., Bitarello, B.D., Schiöth, H.B., Hofreiter, M., Stadler, P.F., Prüfer, K., Lambert, D., Kelso, J. and Schöneberg, T. (2015) Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology, 16, 147 (published online 23rd July 2015, doi: 10.1186/s13059-015-0711-4).
  • Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., Raczky, P., Anders, A., Pietrusewsky, M., Rollefson, G., Jovanovic, M., Trinhhoang, H., Bar-Oz, G., Oxenham, M., Matsumura, H. and Hofreiter, M. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS One, 10 (6), e0129102 (published online 18th June 2015, doi: 10.1371/journal.pone.0129102 eCollection 2015).
  • Xenikoudakis, G., Ersmark, E., Tison, J.L., Waits, L., Kindberg, J., Swenson, J.E. and Dalén, L. (2015) Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 24 (13), 3441-54 (published online 4th June 2015, doi: 10.1111/mec.13239).
  • Springer, M.S., Signore, A.V., Paijmans, J.L., 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., Hofreiter, M. and Campbell K.L.(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 (published online 4th June 2015, doi: 10.1016/j.ympev.2015.05.022).
  • Paijmans, J.L.A., Fickel, J., Courtiol, A., Hofreiter, M. and Förster, D.W. (2015) Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Molecular Ecology Resources, 16 (1), 42-55 (published online 27th April 2015, doi: 10.1111/1755-0998.12420).
  • Zancolli, G., Baker, T.G., Barlow, A., Bradley, R.K., Calvete, J.J., Carter, K.C., de Jager, K., Owens, J.B., Price, J.F., Sanz, L., Scholes-Higham, A., Shier, L., Wood, L., Wüster, C.E. and 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 (6), 188. (doi: 10.3390/toxins8060188).
  • Alter, S. E., Meyer M., Post, K., Czechowski, P., Gravlund, P., Gaines, C., Rosenbaum, H., Kaschner, K., Turvey, S.T., van der Plicht, J., Shapiro, B. and Hofreiter, M. (2015) Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100. Molecular Ecology, 24 (7), 1510-1522 (published online 9th March 2015, doi: 10.1111/mec.13121).
  • Knapp, M., Lalueza-Fox, C. and Hofreiter, M. (2015) Re-inventing ancient human DNA. Investigative Genetics, 6, 4 (doi: 10.1186/s13323-015-0020-4, eCollection 2015).
  • Welcker, F., Collins, M.J., Thomas, J.A., Wadsley, M., Brace, B., Cappellini, E., Turvey, S.T., Reguero, M., Gelfo, J.N., Kramarz, A.,  Burger, J., Thomas-Oates, J., Ashford, D.A., Ashton, P., Rowsell, K., Porter, D.M., Kessler, B., Fisher, R., Baessmann, C., Kaspar, S., Olsen, J., Kiley, P., Elliot, J., Kelstrup, C., Mullin, V., Hofreiter, M., Willerslev, E., Hublin, J.-J., Orlando, L., Barnes I. & MacPhee, R.D.E. (2015)  Ancient proteins resolve the evolutionary history of Darwin's South American ungulates. Nature, 522 (7554), 81-84 (published online 18th March 2015, doi: 10.1038/nature14249).
  • Thorpe, R.S., Barlow, A., Malhotra, A. and Surget-Groba, Y. (2015) Widespread parallel population adaptation to climate variation across a radiation: implications for adaptation to climate change. Mol Ecol 24 (5), 1019-30 (published online 16th February 2015, doi: 10.1111/mec.13093).
  • Xiang, H., Gao, J., Yu, B., Hofreiter, M. and Zhao, X. (2015) Reply to Peters et al.: Further discussions confirm early Holocene chicken domestication in northern China. Proc. Natl. Acad. Sci. U S A, 112 (19), E2416 (published online 17th April 2015; doi: 10.1073/pnas.1503956112).
  • Germonpré, M., Sablin, M.V., Lázni?ková-Galetová, M., Després, V., Stevens, R.E., Stiller, M., and Hofreiter, M. (2015) Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey (2014). Journal of Archaeological Science, 54, 210-216 (DOI:10.1016/j.jas.2014.11.035).
  • Xiang, H., Hofreiter, M. and Zhao, X. (2015) Reply to Peng et al.: Archaeological contexts should not be ignored for early chicken domestication. Proc. Natl. Acad. Sci. U S A, 112 (16), E1972–E1973 (20th March 2015; doi: 10.1073/pnas.1502207112).
  • Hagelberg, E., Hofreiter M. and Keyser, C. (2015) Ancient DNA: the first three decades. Phil Trans R Soc B, 370 (1660), 20130371 (doi: 10.1098/rstb.2013.0371).
  • Ludwig, A., Reissmann, M., Benecke, N., Bellone, R., Sandoval-Castellanos, E., Cieslak, M., Fortes, G.G., Morales-Muñiz, A., Hofreiter, M. and Pruvost, M. (2015) Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses. Phil Trans R Soc B, 370 (1660), 20130386 (doi: 10.1098/rstb.2013.0386).
  • Teasdale, M.D., van Doorn, N.L., Fiddyment, S., Webb, C., O'Connor, T., Hofreiter, M., Collins, M.J. and Bradley, D.G. (2015) Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing. Phil Trans R Soc B, 370 (1660), 20130379 (doi: 10.1098/rstb.2013.0379).
  • Elsner, J., Schibler, J., Hofreiter, M. and Schlumbaum, A. (2015) Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland. Archaeological and Anthropological Sciences, 1-11 (DOI 10.1007/s12520-014-0213-4)

 

2014

  • Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., Fumagalli, M., Raghavan, M., Seguin-Orlando, A., Korneliussen, T., Velazquez, A.M.V., Stenderup, J., Hoover, C.A., Rubin, C.J., Alfarhan, A.H., Alquraishi, S.A., Al-Rasheid, K.A.S., MacHugh, D.E., Kalbfleish, T., MacLeod, J.N., Rubin, E.M., Sicheritz-Ponten, T., Andersson, L., Hofreiter, M., Marques-Bonet, T., Gilbert, M.T.P., Nielsen, R., Excoffier, L., Willerslev, E., Shapiro, B. and Ludovic Orlando, L. (2014) Prehistoric horse genomes reveal the genetic foundation and cost of domestication.  Proc. Natl. Acad. Sci. U S A, 111 (52), E5661-9 (published online 15th December 2014; doi: 10.1073/pnas.1416991111).
  • Hofreiter, M., Paijmans, J.L.A., Goodchild, H., Speller, C.F., Barlow, A., Fortes, G.G., Thomas, J.A., Ludwig, A. and Collins, M.J. (2014) The future of ancient DNA: Technical advances and conceptual shifts. BioEssays, 37 (3), 284-293 (published online 21st November, doi: 10.1002/bies.201400160).
  • Xiang, H., Yuan, J., Gao, J., Yu, B., Luo, Y., Zhou, H., Cai, D., Zhang, Y., Chen, X., Wang, X., Hofreiter, M. and Zhao, X. (2014) Early Holocene chicken domestication in northern China. Proc. Natl. Acad. Sci. U S A, 111 (49), 17564-9 (published online 24th November 2014; doi: 10.1073/pnas.1411882111).
  • King, T.E., Gonzalez Fortes, G., Balaresque, P., Thomas, M.G., Balding, D., Maisano Delser, P., Neumann, R., Parson, W., Knapp, M., Walsh, S., Tonasso, L., Holt , J., Kayser, M., Appleby, J., Forster, P., Ekserdjian, D., Hofreiter  M. and Kevin Schürer, K. (2014) Identification of the remains of King Richard III. Nature Communications, 5, 5631 (published online 2nd December; doi: 10.1038/ncomms6631).
  • Rainford, J.L., Hofreiter, M., Nicholson, D.B. and Mayhew, P.J. (2014) Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects. PLoS One, 9 (10), e109085 (doi: 10.1371/journal.pone.0109085).
  • Gamba, C., Jones, E.R., Teasdale, M.D., McLaughlin, R.L., Gonzalez-Fortes, G., Mattiangeli, V., Domboróczki, L., K?vári, I., Pap, I., Anders, A., Whittle, A., Dani, J., Raczky, P., Higham, T.F.G., Hofreiter, M., Bradley, D.G., and Pinhasi, R., (2014) Genome flux and stasis in a five millennium transect of European prehistory. Nature Communications, 5, 5257 (published online 21st Oct 2014; doi: 10.1038/ncomms6257).
  • Mitchell, K.J., Pratt, R.C., Watson, L.N., Gibb, G.C., Llamas, B., Kasper, M., Edson, J., Hopwood, B., Male, D., Armstrong, K., Meyer, M., Hofreiter, M., Austin, J., Donnellan, S.C., Lee, M.S.Y., Phillips, M.J. and Cooper, A. (2014) Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31 (9), 2322-2330 (published online 30th May 2014; doi: 10.1093/molbev/msu176).
  • Huynen, L., Suzuki, T., Ogura, T., Watanabe, Y., Millar, C.D., Hofreiter, M., Smith, C., Mirmoeini, S. and Lambert, D.M. (2014) Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes). BMC Evol Biol, 14, 75 (published online 14th May 2014; doi: 10.1186/1471-2148-14-75).
  • Horn, S., Prost, S., Stiller, M., Makowiecki, D., Kusnetsova, T., Benecke, N., Pucher, E., Hufthammer, A.K., Schouwenburg, C., Shapiro, B. and Hofreiter, M. (2014) Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Molecular Ecology, 23, 1717–1729 (published online 12th February 2014; doi: 10.1111/mec.12691).
  • Shapiro, B. and Hofreiter, M. (2014) A paleogenomic perspective on evolution and gene function: New insights from ancient DNA. Science, 343, 1236573-1-7 (published online 24th Jan 2014; doi: 10.1126/science.1236573).
  • Stiller, M., Molak, M., Prost, S., Pacher, M., Rabeder, G., Baryshnikov, G., Rosendahl, W., Münzel, S., Bocherens, H., Grandal-d'Anglade, A., Hilpert, B., Germonpre, M., Stasyk, O., Pinhasi, R., Rohland, N., Mohandesan, E., Ho, S.Y.W., Hofreiter, M. and Knapp, M. (2014) Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International, 339-340, 224-231 (published online 5th November 2013; dx.doi.org/10.1016/j.quaint.2013.09.023).
  • Schedina, I.M., Pfautsch, S., Hartmann, S., Dolgener, N., Polgar, A., Bianco, P.G., Tiedemann, R. and Ketmaier, V. (2014) Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data. Journal of Fish Biology 85 (3), 960-4 (published online 25th July 2014, doi: 10.1111/jfb.12470).
  • Zulawski, M., Schulze, G., Braginets, R., Hartmann, S. and Schulze, W.X. (2014) The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification. BMC Genomics 15, 548 (published online 1st July 2014, doi: 10.1186/1471-2164-15-548).
  • Schedina, I.M., Hartmann, S., Groth, D., Schlupp, I. and Tiedemann, R. (2014) Comparative analysis of the gonadal transcriptomes of the all-female species Poecilia formosa and its maternal ancestor Poecilia mexicana BMC Research Notes 7, 249 (published online 17th April 2014, doi: 10.1186/1756-0500-7-249).
  • Struck, T., Purschke, G., Hösel, C., Bleidorn, C., Paul, C., Hill, N., Tiedemann, R., Selbig, J. and Hartmann, S. (2014) Phylogeny and evolution of Annelida based on novel molecular data. Under revision. Pages 143-158 in Deep Metazoan Phylogeny, De Gruyter.
  • Bleidorn, C., Helm, C., Weigert, A., Eeckhaut, I., Lanterbecq, D., Struck, T., Hartmann, S. and Tiedemann, R. (2014) From morphology to phylogenomics: placing the enigmatic Myzostomida in the tree of life. Pages 161-172 in Deep Metazoan Phylogeny, De Gruyter.
  • Knapp, M. and Hofreiter, M. (2014) Ancient Human DNA: Phylogenetic Applications. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester UK. www.els.net [DOI:10.1002/9780470015902.a0005143.pub3].
  • Hofreiter, M. (2014) Ancient DNA. In Oxford Bibliographies in Evolutionary Biology. Editor J. Losos, Oxford University Press, New York, published online 13th January 2014 (DOI: 10.1093/OBO/9780199941728-0036).
  • Jenkins, D.L., Davis, L.G., Stafford, T.W. Jr., Connolly, T.J., Cummings, L.S., Hofreiter, M., Hockett, B., Jones, G.T., Gibbons, S.C., Raghavan, M., Rasmussen, M., McDonough, K., Luthe, I., O’Grady, P.W., Swisher, M.E., White, F., Yohe, R.M. II, Yost, C. and Eske Willerslev, E. (2014) Geochronology, Archaeological Context, and DNA at the Paisley Caves. In The Paleoamerican Odyssey. Editors K.E. Graf, T. Goebel, and M.R. Waters, Center for the Study of First Americans, College Station, Texas.
  • Fortes, G.G. and Paijmans, J.L.A. (2015) Analysis of whole mitogenomes from ancient samples. Pp 179-195 in Whole Genome Amplification (Volume 1347 of the series Methods in Molecular Biology). Editor T. Kroneis, Humana Press, USA.