Polonez

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POLONEZ PROJECT

TitlePhoto
Cultural changes in the evolution of humans and its effects on the epigenetic mechanisms of modern life-style diseases

Funding source
POLONEZ In a combined action of the National Science Centre Poland and the EU’s Horizon 2020 program under the Marie Skłodowska-Curie grant agreement

Grant number
UMO-2015/19/P/NZ7/03971

Principle Investigator
Olaf Thalmann, PhD

Background and research aims
Centuries of research have unraveled the many facets of human’s singularity and with the advances in genetics we are now to infer the molecular foundation of the evolutionary success of our species in unprecedented depth. In particular research involving ancient humans has recently revealed some surprises that dramatically changed the perception of our very own evolution.

Inspired by the seminal work on ancient DNA, I am investigating the epigenetic composition, more precisely the methylomes of Neolithic hunter-gatherers and farmers from Scandinavia to mainly address the over-arching question, if life-style changes in the past have left footprints in the regulatory compartment of genomes. By means of generating high-quality genomes of Neolithic Scandinavians I will reconstruct the methylation patterns preserved in those and allude to adaptive changes between humans living under different life-styles.

Identifying the genetic mechanisms that played a role in the past might lead to new insights relating to diseases associated with nutrition or other modern life-style diseases.

Duration
24 moths

Budget
921,064.00 zł

OLAF THALMANN

Contact

Photo

Current Position
Adiunkt (Assistant Professor) at the Poznan University of Medical Sciences

Current working address
Department of Pediatric Gastroenterology and Metabolic Diseases
Poznan University of Medical Sciences
Szpitalna 27/33, 60-572 Poznan, Poland

Email
othalmann@ump.edu.pl

 


Research

The driving motivation of my research is tightly linked to the quest to understand the mechanisms that shape a species through time and space and explain its genetic adaptability with regard to various environments and climatic epochs.

The focal species of my research involve mainly mammals such as various canids including men’s best friend – the dog, or a critical bioinvader – the raccoon dog. More recently, I added our very own species to this list.

Using a range of genetic data generated from DNA and RNA of a wide variety of sources including ancient and modern materials I aim at reconstructing the respective evolutionary and adaptive histories.

CURRICULUM VITAE
Date of Birth 11.06.1975
Place of Birth Templin, Germany
Current position Adiunkt (Assistant Professor)
Poznan University of Medical Sciences, Poznan, Poland
Current working address Department of Pediatric Gastroenterology and Metabolic Diseases
Poznan University of Medical Sciences
Szpitalna 27/33, 60-572 Poznan, Poland
Degrees
05.03.2007 PhD (Doctor rerum naturalium),
University of Leipzig, Germany
06.09.2001 Diplom (MSc equivalent),
University of Kiel, Germany
Education and Research Experience
Sept. 2016 - present Adiunkt (Assistant Professor)
Poznan University of Medical Sciences,
Poland
Dec. 2015 - Jun. 2016 Informatör/Researcher
EBC University of Uppsala,
Sweden
Oct. 2014 - Nov. 2015 Postdoctoral Researcher
Dept. of Biology, University of Oulu,
Finland
Oct. 2012 - Sept. 2014 Marie Curie Postdoctoral Fellow,
Dept. of Biology, Division of Genetics and Physiology University of Turku,
Finland
Oct. 2010 - Sept. 2012 Postdoctoral Researcher
Dept. of Biology, Division of Genetics and Physiology University of Turku,
Finland
May 2008 - Sept. 2010 Postdoctoral Researcher,
Dept. of Ecology and Evolutionary Biology, University of California Los Angeles,
USA
Feb. 2007 - Apr. 2008 Postdoctoral Researcher,
Primatology Dept., Max Planck Institute for Evolutionary Anthropology, Leipzig,
Germany
Feb. 2003 - Jan. 2007 PhD candidate,
Primatology Dept., Max Planck Institute for Evolutionary Anthropology Leipzig,
Germany
Sept. 2001 - Jan. 2003 Research assistant,
Primatology Dept., Max Planck Institute for Evolutionary Anthropology Leipzig,
Germany
Oct. 1995 - Aug. 2001 Biology Student,
Christian-Albrechts University of Kiel,
Germany
ADDITIONAL PROJECTS

Recent years have witnessed an unprecedented development of technological and theoretical methodologies in evolutionary biology. The emergence of new technologies opens new horizons, enabling us to comprehensively decipher the intriguing network of genotype-phenotype interactions and linking those to environmental and ecological variables.

Men’s Best Friend - the when, where and how of dog domestication

PhotoIt is somewhat difficult to comprehend how the morphological uniformity of grey wolves gave rise to the outstanding variation prevalent in modern dogs. An intriguing approach to this problem is to investigate the genetic composition of ancient wolves and dogs, basically going back in time and elucidate the status quo in dog domestication. This would provide a baseline of variation that artificial selection could have worked upon during domestication. As part of an international collaboration I am currently involved in a project that assembles the genomic composition of numerous Pleistocene canids of global distribution. An important milestone of this project is the generation of the respective complete mitochondrial genomes. We recently completed this task by compiling some 60 ancient canid mito-genomes, of which the analyses suggest some intriguing population history and canid movement in the past.

I further plan to exploit a unique selection of canid material in order to address questions with relevance to dog domestication and genetics of hybridization alike.

Euroinvaders - new lights into the genetic mechanisms of bioinvasions

PhotoA Marie Curie fellowship allowed me to start studying a fascinating aspect of evolution: bioinvasions. The raccoon dog (Nyctereutes procyonoides) is an intriguing mammal that severely affects endemic biodiversity while thriving in new environments. The species’ unique evolutionary history was primarily facilitated by its ability to quickly adapt and is tightly linked to humans. While previous research has provided some fundamental knowledge of the ecological and environmental conditions the species has adapted to, we lack a crucial understanding of the genetic mechanisms that render such a dramatic expansion possible.

Together with European and Asian collaborators, we currently analyze the complete transcriptomes of European and Asian raccoon dogs in order to identify candidate loci selection has acted upon.

PUBLICATIONS
  • “Prediction of harmful substitutions on mitochondrial OXPHOS genes: test of habitat-dependent and demographic effects in euryhaline fish”
    Vasemägi A., Sulku J., Bruneaux M., Thalmann O., Mäkinen H., Ozerov M.
    Ecology and Evolution 7:3826-3835. 2017

  • “Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species”
    Koepfli K-P., Pollinger J., Godinho R., Robinson J., Lea A., Hendricks S., Schweizer R.M., Thalmann O., Silva P., Fan Z., Yurchenko A.A., Dobrynin P., Makunin A., Cahill J.A., Shapiro B., Álvares F., Brito J.C., Geffen E., Leonard J.A., Helgen K.M., Johnson W.E., O’Brien S.J., Van Valkenburgh B., Wayne R.K.
    Current Biology 25:1-8. 2015

  • “Development and characterization of SNP markers in Nazca boobies using Ion Torrent™ sequencing and High Resolution Melt analysis”
    Thomassen H.A, Tompkins E.M., Thalmann O, Anderson D.J. and Foerster K.
    Conservation Genetics Resources. 2015

  • “Attempted DNA extraction from a Rancho La Brea Columbian Mammoth (Mammuthus columbi): Prospects for ancient DNA from asphalt deposits”
    Gold D.A., Robins J., Farrell A.B., Harris J.M., Thalmann O. and Jacobs D.K.
    Ecology and Evolution 4:329. 2014

  • “Complete mitochondrial genomes of ancient canids suggest a European ancestry of domestic dogs”
    Thalmann O., Shapiro B., Cui P., Schuenemann V.J., Sawyer S.K., Greenfield D.L., Germonpré M.B., Sablin M.V., López-Giráldez F., Domingo-Roura X., Napierala H., Uerpmann H-P., Loponte D.M., Acosta A.A., Giemsch L., Schmitz R.W., Worthington B., Buikstra J.E., Druzhkova A., Graphodatsky A.S., Ovodov N.D., Wahlberg N., Freedman A.H., Schweizer R.M., Koepfli K-P., Leonard J.A., Meyer M., Krause J., Pääbo S., Green R.E. and Wayne R.K.
    Science 342:871. 2013

  • “Ancient DNA analysis affirms the canid from Altai as a primitive dog”
    Druzhkova A.S*, Thalmann O.*, Trifonov V.A., Leonard J.A., Vorobieva N.V., Ovodov N.D., Graphodatsky A.S. and Wayne R.K.
    PLoS One 8(3): e57754. 2013

  • “A comparison of brain gene expression levels in domesticated and wild animals”
    Albert F.W, Somel M, Carneiro M., Aximu A., Halbwax M., Thalmann O., Blanco-Aguiar J.A., Plyusnina I.Z., Trut L., Villafuerte Fernandez R., Ferrand N., Kaiser S., Jensen P., Paabo S.
    PLoS Genetics 8(9). 2012

  • “Efficient recovery of whole blood RNA – a comparison of commercial RNA extraction techniques for high-throughput applications”
    Schwochow D., Serieys L.E.K., Wayne R.K. and Thalmann O.
    BMC Biotechnologies 12:33. 2012

  • “Microsatellites in Historic and Ancient DNA”
    Arandjelovic M. and Thalmann O.
    eLS (invited review). 2012

  • “Historical sampling reveals dramatic demographic changes in western gorilla populations”
    Thalmann O.*, Wegmann D.*, Spitzner M., Arandjelovic M., Guschanski K., Leuenberger C., Bergl R.A., Vigilant L.
    BMC Evolutionary Biology 11:85. 2011

  • “Solving a Darwinian Mystery: Evolutionary History of the Falkland Island Wolf”
    Slater G. J.*, Thalmann O.*, Leonard J.A., Schweitzer R.M., Koepfli K-P., Pollinger J.P., Rawlence N.J., Austin J.J., Cooper A., Wayne R.K.
    Current Biology 19: R937-R938. 2009

  • “Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples”
    Arandjelovic M., Guschanski K., Schubert G., Harris T.R., Thalmann O., Siedel H., Vigilant L.
    Molecular Ecology Resources 9(1): 28-36. 2009

  • “Genetic variation in Gorillas”
    Thalmann O.
    PhD thesis, University of Leipzig, Germany. 2007

  • “The complex evolutionary history of gorillas: insights from genomic data”
    Thalmann O., Fischer A., Lankester F., Pääbo S. and Vigilant L.
    Molecular Biology and Evolution 24. 146-158. 2007

  • “Demographic history and genetic differentiation in Great Apes”
    Fischer A., Pollack J., Thalmann O., Nickel B. and Pääbo S.
    Current Biology 16. 1133-1138. 2006

  • “Nuclear insertions help and hinder inference of the evolutionary history of gorilla mtDNA”
    Thalmann O., Serre D., Hofreiter M., Lukas D., Eriksson J. and Vigilant L.
    Molecular Ecology 14. 179-188. 2005

  • “Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes”
    Thalmann O., Hebler J., Poinar H.N., Pääbo S. and Vigilant L.
    Molecular Ecology 13. 321-335. 2004