Doctoral position - Understanding animal domestication using palaeogenomics

Department/Institute: LMU Palaeogenomics Group, Institute for Domestication Research

Subject areas/Research fields: evolutionary biology, genetics, archaeology 

Keywords: ancient DNA, animal domestication, genomics, dogs

Name of supervisor: Prof. Laurent Frantz

Project title: Understanding animal domestication using palaeogenomics

Project description:

Animal domestication was one of the most important transitions in human history, beginning with the long-term association between hunter–gatherers and wolves more than 15,000 years. This long term association with people resulted in new selective pressures which led to substantial biological changes in animal species (e.g. behavior, appearance, circadian rhythm etc.), as well as in people (e.g. via spread of zoonotic disease etc). 

Genomic data obtained from modern domestic animals can be used to address questions about the geographical and temporal origins as well as to understand the strength and consequences of these selective pressures on the genome. Genomic information obtained from living animals, however, provides only a contemporary snapshot of a long-term evolutionary process. Domestic species have also dramatically changed in less than a century, e.g. chicken growth rate has tripled in the last 50 years and cranial shape variation across modern dog breeds now exceeds the range of differences observed across the entire order of Carnivora. This makes it difficult to make inferences about domestication based solely on the analyses of modern population data.

In the past decade, novel molecular techniques have enabled access to genetic information from past populations (palaeogenomics). This has allowed us to obtain genomes of animals and that of the pathogens they were infected with, using DNA extracted from ancient skeletal remains, found at archeological and palaeontological sites. Palaeogenomics allows us to generate genomic time series, and answer questions related to the origin and the spread of domestic populations across the globe, to assess how animals adapted to the myriad of environments in which they were introduced, or to better understand ancient events of zoonoses. 

The student will be integrated in our team based at LMU and London, and will be expected to take part in international collaborative networks, including with groups in Oxford, the NIH, and UCL (among others). They will be given the opportunity to choose one of multiple specific projects focusing on the evolutionary history of domestic species and that of their pathogens. This includes, projects related to the temporal and geographic origin of domestic dogs, the process of fertilization in pigs (i.e. what happened to genome when species go back to the ‘wild’), or the study of the evolution of pathogenic species that affect both animals and people (e.g. evaluate the role of domestic pigs as zoonotic pathogen reservoirs in the past).

References:

1. Fiddaman SR et al. (2023) ‘Ancient chicken remains reveal the origins of virulence in Marek’s disease virus’. Science 382, 1276–1281.
2. Jamieson A et al. (2023) ‘Limited historical admixture between European wildcats and domestic cats’. Curr. Biol. 33, 4751–4760.e14.
3. Lin AT et al. (2023) `The history of Coast Salish ‘woolly dogs’ revealed by ancient genomics and Indigenous Knowledge`. Science 382, 1303–1308.
4. Bergström, A. et al. (2022) ‘Grey wolf genomic history reveals a dual ancestry of dogs’, Nature, 607(7918), pp. 313–320.
5. Frantz, L.A.F. et al. (2020) ‘Animal domestication in the era of ancient genomics’, Nature reviews. Genetics, 21(8), pp. 449–460.
6. Bergström, A. et al. (2020) ‘Origins and genetic legacy of prehistoric dogs’, Science, 370(6516), pp. 557–564.
7. Feuerborn, T.R. et al. (2021) ‘Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal’, PNAS, 118(39). 
8. Plassais, J. et al. (2022) ‘Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids’, Current biology: CB, 32(4), pp. 889–897.e9.
9. Perri, A.R. et al. (2021) ‘Dog domestication and the dual dispersal of people and dogs into the Americas’, PNAS, 118(6). 
10. Perri AR et al. (2021) ‘Dire wolves were the last of an ancient New World canid lineage’. Nature 591, 87–91.
11. Frantz, L.A.F. et al. (2019) ‘Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe’, PNAS 116(35), pp. 17231–17238.
12. Ní Leathlobhair, M. et al. (2018) ‘The evolutionary history of dogs in the Americas’, Science, 361(6397), pp. 81–85.

For further information, please contact: Prof. Laurent Frantz, laurent.frantz@lmu.de

Reseach group website: https://www.animal-palaeogenomics.com/

Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM)