Coronavirus Dansk / English

Deciphering the evolutionary history of horses, asses and zebras – University of Copenhagen

2 December 2014

Deciphering the evolutionary history of horses, asses and zebras

Whole genome-dataset of horses, zebras, and asses unveils their evolutionary origins, revealing genes underlying their specific adaptations, and multiple instances of gene-flow despite drastic differences in chromosomal structure.

The study, which was carried out by an international team of researchers, revealed not only a highly dynamic population history over the last 4.5 million years, but also uncovered multiple cases of gene-flow across a number of species showing extensive chromosomal rearrangements. This suggests that the multiple changes in the structure of chromosomes did not preclude species interbreeding, in contrast to what previous models of speciation have assumed for equids.

The study was led by the Centre for GeoGenetics at the University of Copenhagen, in collaboration with scientists from 8 additional international institutes, including the University of Kentucky and the University of California, Berkeley. It has been published in the scientific journal PNAS on 1. December 2014.  

Equids, an iconic group of mammals

Horses, zebras, and asses represent the only living members of the equid family, all of which belong to a single genus, Equus. This family originated from a dog-sized ancestor that lived in Northern America some 55 millions ago and flourished into a large number of species during the Tertiary period. Some crossed the Bering Strait and discovered the Old World, where they diversified their diet, mixing grazing and browsing or becoming full grazers.

Zebra in the Zoological Gardens of Copenhagen. Photo: Frank Rønsholt.

Their evolutionary history is well documented in the paleontological record and represents a textbook example of evolution. Most of this past diversity is now gone and all extant equids originate from a most recent common ancestor that lived ~4.5 million years ago. Two such species, horses and donkeys, were domesticated some 5,500 years ago and greatly impacted human history. Says Dr Ludovic Orlando, Assistant Professor at the Centre for GeoGenetics, who led the study:

- Equids are fascinating. A large number of species radiated within the last 4.5 million years, 7 of which are still living. They expanded from the Americas into Eurasia and Africa. They colonized very different environments, from the cold Arctic to the tropics. In comparison, hominins and gorillas, chimpanzees and bonobos arose within the last 13 millions years. With more species emerging in a shorter time period and surviving until now, equids offer an ideal model for understanding the evolutionary process in greater detail.

Whole-genome sequencing unravels the equid family tree

With the publication of a whole-genome dataset encompassing all living members of Equus, researchers at the Danish Centre for GeoGenetics aimed to cast light upon the recent history of this iconic group of quadrupeds. The research team took advantage of state-of-the-art methods in DNA sequencing to characterize high-quality genomes from zoo animals of the Somali wild ass, the onager, the Tibetan kiang and all three living species of zebras (the plains zebra, the mountains zebra and the Grevyi’s zebra). The team did not limit its efforts to only living species but also reconstructed the genome of a now extinct equine species, the quagga zebra. Says Andaine Seguin-Orlando, PhD student at the Centre for GeoGenetics, co-leading author of the study:

- The quagga zebra was once found in great numbers in South Africa but was hunted to extinction at the beginning of the 20th century. This enigmatic species showed a characteristic zebra stripe pattern only in the front part of the body in contrast to other zebras. Ancient DNA research actually started in 1984 following the sequencing of a short DNA fragment from the extinct quagga zebra.

Says Dr Ludovic Orlando:

- It is amazing to realize how much progress has been made in only 30 years and that we are now able to characterize their entire genome sequence. The genome confirmed the early work from the 1980s, showing that the extinct quagga was closely related to plains zebras. It also revealed some specific genes that were selected in each population after their split, some 300,000 years ago.

By taking advantage of this dataset to reconstruct a phylogenetic tree based on almost 20,000 protein-coding genes, the scientists at the Centre for GeoGenetics were indeed able to resolve the evolutionary relationship of the surviving equids and to identify the evolutionary genetic changes that occurred on each individual lineage. Says, Mikkel Schubert, PhD student at the Centre for GeoGenetics, co-leading author of the study:

- Having whole genomes in hand, we were not limited in sequence information. This allowed us to reconstruct the phylogeny and date population divergences with much greater confidence than has previously been possible. 

Says Ernest Bailey, Professor at the Gluck Equine Research Center, who participated in the study:

- Genetic changes at SCL9A4, a channel involved in pH regulation known to counter adverse environmental conditions, appear to have been adaptive in plains zebras. This might partly explain how this species can manage to cope with its wide range of environmental conditions. Adaptive changes at SEMA5A are unique to the extinct quagga zebra, and could be responsible for cranial and cognitive specific to this group.

Says Professor Rasmus Nielsen, from the Department of Integrative Biology at UC Berkeley:

- By revealing what changes were selected along the different branches of the evolutionary tree, such studies start to reveal the genetic makeup of each species. It advances our understanding of what genetic changes make the different species look, live and behave differently. 

Surprising interbreeding despite apparent genetic barriers

The genomes of the different equine species did not solely diverge at the sequence level as numerous large-scale rearrangements have been found in their chromosomes. Says, Dr Teri Lear from the Gluck Equine Research Center, who carried out cytogenetic characterization of the onager as part of the study: 

- In contrast to humans and chimpanzees which show quite similar karyotypes, the different equine species show extreme differences in their chromosome numbers. It can range from 16 pairs in the Hartmann’s zebra, to 33 pairs in Przewalski’s horses. It is much more plastic than what has been found between humans and chimpanzees, which only differ by one pair of chromosomes. In addition, many chromosomal segments have been shuffled around. 

This rapid accumulation of chromosomal changes has long been thought to act as a barrier to interbreeding between species and could therefore have represented speciation drivers, genetically isolating populations and ultimately leading to the emergence of a new species. However, when the research team looked for traces of admixture in their genome dataset, the results came as a surprise: several species show evidence of admixture, suggesting that such massive chromosomal rearrangements did not totally abolish their capacity to reproduce with each other. Says Hákon Jónsson, PhD student at the Centre for GeoGenetics, co-leading author of the study:

- Because of the massive differences in the genome organization, we expected to find no evidence for admixture between equine species. Yet, we find multiple cases of gene flow, implying that cross-species hybridization resulted in fertile offspring in evolutionary times. The most prominent signal concerns the Somali wild ass and the Grevyi’s zebra, two territorial species whose geographic range used to overlap in Eastern Africa. This is in stark contrast with previous models assuming that karyotypic changes would completely stop reproduction between species. 

Professor Rasmus Nielsen and Professor Eske Willerslev conclude:

- That mules and hinneys are generally sterile is perhaps the most popular example for illustrating the concept of species in biology classes. Genomics tells us that the species barrier is not always waterproof and now invites us to reinvestigate important biological questions, such as what drives the origin of species.