1 | INTRODUCTION
The domestic horse (Equus caballus ) is a culturally, economically, and historically important domesticated animal. The domestication of the horse in central Asia ~5,000 years ago is one of the most significant achievements of human civilization (Outram et al., 2009). Since then, horse has been extensively used in agriculture, transportation, war, and sports (Kalbfleisch et al., 2018). A significant change of the impact of domestication on animals is mainly in nutrition and behavior, but the impact on the large parasites living in the host remains unknown. The genetic architecture and selection are key indicators of evolution aiming to understand how natural selection and artificial selection can lead to lineage divergence and speciation(Jones et al., 2012). The genetic differences between populations can reveal a lot about the basic evolutionary process due to changes in the environment. (Schluter, 2009). Studying the adaptation of parasites along with host domestication is of great significance for understanding the host-parasite interactions.
Equine roundworms are large parasitic nematodes that predominantly infect foals and weanlings. The Equus species, such as horse (Equus caballus ), zebra (Equus zebra ) and donkey (Equus asinus ), are the reservoir hosts for Parascarisspp. Despite their close kinship, the extent of domestication in these hosts are vastly different. Horses have been domesticated for thousands of years and are intimately linked to human activity. Comparatively, donkeys are far less domesticated than horses, while zebra has not been domesticated so far. In addition, the nutritional requirements of the three are also different. For example, donkeys have much lower energy and protein requirements than those of other equids(Martin-Rosset, 2018), and even the metabolic response during exercise will differ depending on the level of food given to the horse (Jansson & Lindberg, 2012), which may also be a challenge for parasites. Extensive genetic diversity provides the genetic basis for the adaptive evolution of nematodes, but a successful evolution will also come at a cost to the host (Hay et al., 2017). Roundworms’ underlying genetic diversity contributes to their ability to adapt and undergo selective evolution. Understanding these processes, as well as the key environmental factors that lead to selection, is crucial to comprehend the evolution of parasites (Salle et al., 2019).
The control of parasitic nematodes feeding on animal relies almost exclusively on anthelmintic drugs, which is proved to be effective in the short-term management, but the long-term effectiveness has been questioned due to the widespread emergence of drug resistance (Kaplan & Vidyashankar, 2012). There is widespread concern about the risk associated with relying on anthelmintics with hundreds of millions of doses being donated and used every year(McManus, 2018). In general, levels and spectrum of anthelmintic resistance are less severe in parasites of horses, however, the same issues persist, and they seem to be worsening (Kaplan, 2004; Kaplan et al., 2004; Traversa et al., 2009). It is now clear that the effective method for long-term control of nematodes is to improve pasture (or nature reserve) management and scientific genetic monitoring, rather than simply using chemical methods (Kaplan & Vidyashankar, 2012). In recent years, genome scanning has become an effective means to reveal the genetic determinants of habitat differences in some organisms. Since less introgression occurs in the selected loci, they exhibit lower polymorphism than other regions of the genome, which enables the formation of highly divergent regions that serve as the genetic foundation for divergence (Nosil, Vines, & Funk, 2005; Wu, 2001). Here we analyzed the genome characteristics ofParascaris spp. populations dwelling on three main hosts: horse (Equus caballus ), zebra (Equus zebra ) and donkey (Equus asinus ). To the best of our knowledge, here we present the first report on the recent divergence of Parascaris spp. populations, and speculate that it may be linked to roundworm host preference. Meanwhile, the role of selection (natural or man-made selection) in the population was also evaluated at the genetic level. This work is of great significance for changing the current ”one size fits all” roundworm taxonomy, and opens a new era of precise monitoring of roundworm evolution.