The so far most exhaustive population genetics study on donkey evolution was recently published in Nature Communications. The study sheds light on when, where and how donkey domestication occurred, and on the reproductive management effects on the species variability. The study, led by Dr Changfa Wang from the Shandong Academy of Agricultural Sciences and researchers from other Chinese institutions, included the participation of researcher Jordi Jordana from the Universitat Autònoma de Barcelona (UAB) and CRAG researchers Marcel Amills and Antonia Noce.
The study involved the de novo assembly of a high-resolution chromosome-level reference genome of one male donkey and the sequencing of the genomes of 126 domestic donkeys from nine countries, and 7 wild asses (6 from Asia and one from Africa).
The research published confirms the results of a previous study published in 2004 using mitochondrial DNA (inherited only through the mother), which indicated that the donkey was domesticated in Northeast Africa 6000 years ago from the African wild ass (Equus africanus), and not from the Asian wild ass (Equus hemionus). The authors of the new study point out that there is not yet enough evidence to state whether the domestication process took place in one or more geographic areas, but with the genetic and archeaological information available to date, the most plausible place for this domestication would have been Egypt.
The study distinguishes between two very different genetic lineages, which separated some 6,000 years ago: one corresponded to the asses of tropical Africa (Kenya, Ethiopia, Nigeria) and the other to northern Africa and Eurasia (Egypt, Spain, Iran, Kyrgyzstan and China). "Iberian asses belong to this second group, demonstrating greater affinity with subpopulations in Egypt, clearly and genetically differentiated from the Asian populations", Jordi Jordana points out.
A third differentiated group is that of Oceania, represented by Australia. This strong differentiation would be the result of an important founding effect, caused by the limited number of individuals transported from the British colonies some 200 years ago, as well as by the effects of a prolonged geographic isolation and elevated genetic drift load. Nevertheless, the Australian population reveals to be genetically most closely related to the Spanish donkey population, making it clear that it is of European origin.
With regard to Spanish breeds, the study "corroborates the previous conclusions and results, such as the marked common ascendency of the Andalusian and Majorera breed of the Canary Islands, perfectly differentiated in all analyses conducted (autosomal polymorphisms, mitochondrial DNA and Y chromosome), and from all other black coat breeds found in Spain (Catalan, Balearic, Zamoran-Leonese and the Enkarterri donkey in the Basque Country)", says Jordi Jordana.
Genetic consequences of the selection process
The study reveals that, contrary to what had been previously described, there was a significant reproductive bias in the donkey’s evolutionary history, as a result of the selective process that took place during or after domestication. “The variability of the donkey Y chromosome is pretty low, much lower than the mitochondrial variability. This suggests that, historically, as has already been shown in the horse, a low number of male donkeys were intensively used as breeders, mating with numerous females”, explains UAB Associate Professor and CRAG researcher Marcel Amills.
Furthermore, the researchers also studied the imprint of selection on two clearly differentiated coat pigmentation patterns in donkeys: the Dun pattern, more ancestral, characterized by a strong dilution of pigmentation - individuals are gray or light chestnut-, and the so-called non-Dun, in which this dilution of the coloration does not exist and, therefore, the individuals, essentially domestic donkeys, display non-diluted black or chestnut coat colors.
The research team found that a mutation in the TBX3 gene is responsible for the non-Dun coloration in donkeys. In horses, two different mutations from that observed in donkeys, but located in the same gene, are responsible for the non-Dun coloration. Hence, this work has shown that the biochemical basis of pigmentation dilution is very similar in horses and donkeys, since in both species the TBX3 gene affects the symmetry of the distribution of pigment granules in the hair.
“This result shows that the process of selection of undiluted colorations that took place in horses and donkeys thousands of years ago, possibly at the beginning of domestication, convergently targeted the same gene (TBX3) in both species”, says Marcel Amills. “The reason for selecting coat color is not known. Perhaps on a whim or for practical reasons, such as facilitating the location of animals, or for cultural or religious reasons”, he adds.
“The domestication process implied changes in morphology, color, reproduction and behaviour of the domesticated species through a selection led by humans, but it is unknown whether this selection acted on different genes in each species or if it affected the same groups of common genes in different domesticated species. As mentioned before, in the case of coloration in horses and donkeys, the selection acted on the same gene (TBX3) in both species”, concludes Marcel Amills.
Conducting the study
In order to conduct the study, combining different molecular techniques, researchers first sequenced the genome of a domestic donkey with a resolution and quality far higher than that of other studies. Following, they sequenced the genomes of 126 domestic donkeys from Europe (Spain, 6 breeds), Asia (China, Iran, Kyrgyzstan), Africa (Egypt, Kenya, Ethiopia and Nigeria), and Oceania (Australia). This source of information was combined with 7 complete genomes of wild asses (3 hemione, 1 onager, 2 kiang and 1 Somalian wild ass), which had already been described.
In contrast to previous studies, researchers used millions of genetic markers (17 million autosomal polymorphisms), uniformly distributed throughout the donkey's genome. The also compared the genetic diversity of the donkeys at mitochondrial and Y-chromosome levels (13,000 polymorphisms), to verify whether or not there was a reporductive bias affecting the variability of the species.
Article of Reference: Changfa Wang et al. Donkey genomes provide new insights into domestication and selection for coat color (2020) Nature Communications https://doi.org/10.1038/s41467-020-19813-7