PhD defense: Charleen Gaunitz

Reconstructing the History of Biological Changes Underlying Extinction and Domestication Processes - A Tale from Ancient Horse Genomics

Supervisor: Prof. Ludovic Orlando, UCPH and Univ. Toulouse

Defense Committee Chair: Assoc. Prof. Anders J. Hansen, UCPH

Censor:
Prof. Ian Barnes (Natural History Museum London, UK) Assoc.
Prof. Gabriella Lindgren (SLU, Sweden)

Summary
Among all animals domesticated, the horse undoubtedly shaped and transformed human societies in the most tremendous way. It revolutionised the means of human mobility, transportation, agriculture and warfare. And yet, the exact timing and location of its domestication remain enigmatic. The underlying evolutionary processes that transformed the wild horse into a domestic horse, represented by over 500 distinct breeds living today, are still not fully understood and are difficult to reconstruct using solely archaeozoological and modern genetic data. Yet, with archaeogenetics, we have the possibility to access the genetic code of ancient horses and follow their population history.

This PhD project leveraged on the latest methodological and computational advances in ancient DNA research in order to create the first comprehensive spatio-temporal dataset based on whole ancient horse genomes to (1) explore the geographical origin and timing of horse domestication and (2) to address the suite of biological modifications accompanying the transformation of wild horses into domestic horses.

By examining the genetic diversity of ancient Scythian horses and modern domestic horses, we found that the common hypothesis that domesticated horses descend from only a limited number of stallions is not accurate. Instead, a demographic collapse, occurring over the last 2,300 years, is possibly responsible for the demise of the Y-chromosomal diversity in modern horses. This loss of genetic diversity was simultaneously accompanied by an increase of deleterious mutation load in modern domestic horses. Besides, scans for ancient selection signatures revealed the footprint of adaptation in genes associated with cognitive behaviour and neural crest development, supporting the domestication syndrome theory, which provides a unified framework to explain all morphological changes commonly observed in domesticated animals.

Further characterisation of 20 horse genomes from the Botai site, presenting the earliest documented evidence for horse domestication, revealed that all ancient and modern domesticated horses younger than ~ 4,100 years descend from a different horse lineage other than Botai. That implies (1) the existence of a second horse domestication centre or (2) an almost complete replacement of the Botai ancestry during the expansion process of the horse population post-Botai through introgressive capture. Finally, this PhD project revealed that the Przewalski’s horse does not represent the last true remaining wild horse on earth as commonly thought. Much more it is the feral descent of the horses that were exploited and first domesticated at the Botai site.