Profile

Career

Research

Overview

My research focuses on the effect environmental changes have on genetic diversity,adaptations and population dynamics in animals. I am especially interested in theuse of ancient DNA sequences to directly observe changes in the genetic make-up ofpopulations. Using this approach we could detect complete population replacementsand migrations that could not be deciphered using traditional methodologies. We havedeveloped a variety of technologies that allow using next generation DNA sequencing(NGS) for projects involving many individuals, which adapts NGS for research inevolutionary biology and population biology. Currently we are focusing on the use ofDNA hybridisation capture technologies for obtaining complete mitochondrial genomesand large targeted nuclear DNA data sets for phylogenetic, population genetics andfunctional genetics studies using fossil DNA.

Discoveries

We found evidence that times of environmental change seem to also be times ofelevated speciation rates, but at the same time usually times when genetic diversitydeclines. Thus, most species had much higher genetic diversity during the Pleistocenewhen compared to today.

Current projects

• Developing generic capture arrays for targeted high-throughput sequencing ofmammalian mitochondrial genomes and nuclear genes from multiple samples (MarcWadsley; in collaboration with Matthew Collins, Department of Archaeology).
• Investigating genetic diversity over time in Spanish brown and cave bears (GloriaGonzalez Fortes; in collaboration with Aurora Grandal d’Anglade, Universidade daCoruña).
• Studying the phylogenetic position of rare Pleistocene mammals, includingHomotherium and Elephas antiquus (Johanna Paijmans; in collaboration with, amongothers, Jelle Reumer, Museum of Natural History, Rotterdam and Kurt Alt, University ofMainz).
• Functional genetics of cold adaptation in extinct Arctic mammals (together withKevin Campbell, University of Manitoba).
• The genetic effects of horse domestication (together with Arne Ludwig, IZW, Berlin)
• The phylogeny of sharks and rays (together with Gavin Naylor, College ofCharleston)

Research group(s)

Previous visiting researchers and students

Collaborators

Beth Shapiro, UC Santa Cruz

Arne Ludwig, IZW

Matthew Collins, Department of Archaeology, The University of York

Kevin Campbell, University of Manitoba

Hucai Zhang, Yunnan Normal University

Gavin Naylor, College of Charleston

Publications

Selected publications

Pruvost, M. Bellone, R., Benecke, N., Sandoval-Castellanos, E., Cieslak, M., Kuznetsova,T., Morales, A., O’Connor, T., Reissmann, M., Hofreiter, M. and Ludwig, A. (2011)Genotypes of pre-domestic horses match phenotypes painted in Paleolithic works of caveart. Proc. Natl. Acad. Sci. USA, 108 (46): 18626-18630.

Lerner, H, R. L., Meyer, M., James, H. F., Hofreiter, M. andFleischer, R. C. (2011) Multilocus resolution of phylogenyand timescale in the extant adaptive radiation of Hawaiianhoneycreepers. Current Biology, 21 (21): 1838-1844.

Lippold, S., Allentoft, M., Benecke, N., Koepfli, K.-P.,Kuznetsova, T., Ludwig, A., Weinstock, J., Willerslev, E.,Shapiro, B. and Hofreiter, M. (2011) Discovering the lostdiversity of paternal horse lineages using ancient DNA.Nature Communications 2: 450.

Rohland, N., Reich, D., Mallick, S., Meyer, M., Green, R.E.,Georgiadis, N.J., Roca, A., and Hofreiter, M. (2010)

Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation offorest and savanna elephants. PLoS Biology 8 (12): e1000564.

Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G.A., Castaños, P.,Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A.-S., Slatkin, M. and Hofreiter, M.(2009) Coat color variation at the beginning of horse domestication Science 324: 485.

Out now:

Beth Shapiro & Michael Hofreiter (eds): Ancient DNA:

Methods and Protocols

External activities

Editorial duties

• Associated editor for PLoS One
• Associated editor for BMC Evolutionary Biology
• Associated editor of Scientific Reports
• Editorial board member Human Biology
• Editorial board member Investigative Genetics