Genomic signatures of domestication in Old World camelids

During domestication, extensive artificial and natural selection has acted on the genomes of domestic animals. The adaptation to different environmental and anthropogenic pre-defined conditions has resulted in a huge diversity of phenotypes and breeds among our livestock species. Recent advances in whole-genome sequence analysis have made it possible to identify those changes that underlie the transformation process from a wild species to a domesticated. The aim of this project is to investigate for the first time genetic footprints of selection in domestic camels and their wild relatives. Old World camels (Camelini) are one of the most recent species to have been domesticated and today, only small populations of their wild relatives (Camelus ferus) exist in Mongolia and China. Contrary to other livestock animals that have been strongly selected for their specific single traits, the domestication of the "multi-purpose" camels has taken a different course, with little selection for features other than tameness and tolerance of humans. Thus, camels are ideal candidates to study mechanisms related to the "initial stage" of domestication. In our previous work we have detected remarkable variation in the DNA of dromedaries and Bactrian camels worldwide, which might reflect not only demographic expansion after an initial domestication but also ancestral diversity. Based on these observations we hypothesize that (H1 ) the camel genome has been shaped by recent anthropogenic selection (domestication) leaving signals in specific regions, which are discernable by comparative analyses of wild and domestic two-humped camels and dromedaries as well as pre-domestic specimens; and (H2 ) independently of domestication, the evolutionary history of Old World camels has been driven by random processes and environmental adaption with genetic footprints over the whole genome. With this project we expect to gain insights into the genetic mechanisms underlying the domestication process in general and specifically in camels. By defining candidate genes for domestication in camels and comparing them with functional important regions in other mammalian genomes we will increase our knowledge of functional genomics. Our results about the evolutionary history of the Camelini will contribute to the in-situ conservation of the highly endangered wild camels in Mongolia and China, and to the scientific and economic value of the most important domestic species in (semi-) arid regions with increasing desertification.

In the Old World camelids, two varieties of domesticated camels are recognized: the two- humped Bactrian camel (Camelus bactrianus) and the single-humped dromedary (Camelus dromedarius). The critically endangered wild two-humped camels (Camelus ferus) have never been domesticated and exist today only in the Mongolian Gobi desert and in the Chinese Taklamakan and Lop Nur. Archeozoological studies have suggested that domestication of Bactrian camels occurred between 5000 and 6000 years ago. The genetic results from our project show that dromedaries were domesticated approximately 3000 years ago from a small wild population in the Southeast coast of the Arabian Peninsula. Multiple re- stocking from the wild into the early domestic herds increased the diversity until wild dromedaries became extinct around 2000 years ago. Throughout their range camels are bred for a multitude of purposes including meat and milk production, transportation, wool, and sport. Additionally, several camel products, like camel milk, have proven beneficial for human health. Contrary to many other domestic mammals, however, camels do not manifest many of the canonical traits associated with domestication relative to their wild counterparts (e.g. retention of juvenile characteristics, continual reproduction, short maturation period). Therefore, we propose that an investigation of artificial selection in the camel genomes will yield comparably different results from that of other domesticated species. To date, genome sequencing of the Bactrian camel and its extant wild relative, Camelus ferus, has suggested that olfaction may have played an important role during Bactrian camel domestication. However, no dromedary genome existed so far, and certain inferences regarding artificial selection cannot be made from a single individuals genome. In our study, we sequenced 25 camel genomes to medium coverage (~15X), including individuals from all three species. We also sequenced at high coverage (~60X) and assembled de novo the dromedary genome. In addition to a description of the dromedary genome, we investigate how artificial selection and demography have shaped the camel genomes. We also present a genome-wide set of single nucleotide variants for Old World camels and review the potential for high-throughput genotyping and implementation of marker-assisted breeding programs to improve economically relevant traits.