Mitochondrial and nuclear genomes reflect different evolutionary trajectories of two ungulate species: tales from aoudad (Ammotragus lervia) and bighorn sheep (Ovis canadensis) in Texas



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The original focus of this dissertation was solely on desert bighorn sheep (Ovis canadensis) in Texas. With no genetic studies on these populations to date, there was a paucity of information that this study intended to rectify through mitochondrial and nuclear DNA studies. During the initial stages of this endeavor, it became clear that another montane ungulate, aoudad (Ammotragus lervia) also lacked genetic information and directly competed for resources, occupied similar niches, and possibly posed a disease-risk to desert bighorn sheep. Therefore, the aims of this dissertation shifted to examine the genetic diversity, population structure, kinship, connectivity, and other genetic parameters of desert bighorn sheep and aoudad in Texas. Bighorn sheep (Ovis canadensis, Shaw 1804) once numbered 1.5-2 million individuals range-wide, extending from Canada to Mexico (Seton 1929). Populations began to decline with human expansion and settlement in the western U.S. and subsequent establishment of livestock in close proximity to habitats associated with bighorn sheep. Overharvesting for meat and horns, diseases transmitted between domestic sheep and goats to bighorn sheep, predation, and other issues have been recognized as factors associated with declines of bighorn sheep populations (Davis and Taylor 1939, Buechner 1960). Range-wide estimates of bighorn sheep were < 25,000 (Buechner 1960) and both O. c. auduboni and O. c. texiana subspecies already had been extirpated from their respective ranges by the early 20th Century. As a result, several subspecies, populations, and putative genetic units were, or nearly were, extirpated from Colorado, Nevada, New Mexico, North Dakota, Oregon, Texas, South Dakota, Utah, and Washington (Buechner 1960, Bailey 1980, Valdez and Krausman 1999). There exists the potential of geographic isolation for individuals of bighorn sheep as a result of their habitat preference for high-elevation montane areas, making it somewhat unclear as to what constitutes a population. In some cases, albeit rare, bighorn sheep have been known to cross the intervening lowlands from one mountain range to the next (Epps et al. 2018). Consequently, in this proposal, the term ‘population’ is defined as a general reference to bighorn sheep (e.g., the population of bighorn sheep in the Trans-Pecos Ecoregion). The term ‘subpopulation’ is restricted to define individuals that occupy a particular mountain range that is presumably isolated from other ranges (e.g., the subpopulation of bighorn sheep located in the Van Horn Mountains compared to the subpopulation located in the Baylor Mountains). Desert bighorn sheep (DBS) historically occurred in 16 mountain ranges across the Trans-Pecos Ecoregion of Texas (Gould 1962) with an estimated population size of 1,500 individuals in the 1880’s (Cook 1994). Carson and A. T. Jackson reported prehistoric Indian pictographs of DBS in a cave in Victorio Canyon of the Sierra Diablo range (Jackson 1938), indicating DBS inhabited various areas of the Trans-Pecos Ecoregion for some time after human occupation of the region. Further, petroglyphs, which predate pictographs, of DBS are recorded in El Paso, Hudspeth, and Culberson counties (Buechner 1960). During the Biological Survey of Texas, Vernon Bailey collected six bighorn sheep specimens (i.e., complete skulls and/or skins) from Guadalupe and Van Horn Mountains in 1901 and 1902. In Bailey’s first assessment of DBS in Texas and southeastern New Mexico, he classified them as O. c. mexicana based on phenotypic characters (Bailey 1905). However, this taxonomic designation was solely determined using four older rams (4-7 years old). In 1912, Bailey reexamined the bighorn skulls of both rams and ewes and discovered that unique cranial characteristics were prominent in ewes. Further, DBS in Texas and southeastern New Mexico were exceptionally different from O. c. mexicana, O. c. audoboni, and O. c. canadensis based on “extremely narrow” facial regions of the skull, nasals, and palate. This identification of different cranial characteristics led to Bailey reclassify the bighorn sheep in Texas and southeastern New Mexico as a distinct taxonomic unit, O. c. texianus (Bailey 1912). This subspecific designation was later reviewed by Cowan (1940), who acknowledged the cranial differences as suggested by Bailey but demonstrated that these measurements were not supported as statistically inimitable from specimens of O. c. mexicanus from Chihuahua. This finding resulted in synonymizing O. c. texianus under O. c. mexicanus, which was recognized by Miller and Kellogg (1955) of the United States National Museum and remains as such today. Bailey also reported that approximately 500 DBS inhabited the Trans-Pecos region and southeastern New Mexico in the early 1900’s. However, the regional DBS population continued to decline over the next 50 years and by 1959 only 14 DBS remained in the Sierra Diablo range, where extirpation of Texas DBS presumably occurred at some point during the 1960s. Over the next 60 years (1957-present), restoration and translocation efforts by Texas Parks and Wildlife Department (TPWD) reestablished subpopulations in 11 mountain ranges, totaling >1,500 individuals by 2018. Source stock origins for translocations into Texas used individuals of O. c. nelsoni and O. c. mexicanus from Arizona, Nevada, and Utah, and Mexico and some from in-state brood facilities at the Black Gap and Sierra Diablo Wildlife Management Areas (WMA) (Cook 1994). Subsequent intrastate translocations primarily from Elephant Mountain WMA to other areas with suitable habitat (i.e., Black Gap WMA, Nine Point Mesa, etc.) have been ongoing since 2010. The introduction of exotic species into new geographical areas through human-mediated translocations often inflict several direct and indirect ecological impacts on native species (Strauss, Webb, & Salamin, 2006). Of concern in the US, is the fact that aoudad (Ammotragus lervia, Pallas, 1777) are sympatric with native bighorn sheep (Ovis canadensis) (Simpson and Krysl, 1981). During a 1979–1980 survey of exotic big game ungulates in Texas, Harmel (1980) determined that aoudad numbers (n = 3,709) had increased 139% since the 1974 census. A subsequent survey in 1988 (Traweek, 1989) estimated 20,402 individuals in Texas. Mungall & Sheffield (1994) surmised not only were aoudad populations continuing to expand but that aoudad were now common in the Edwards Plateau (50% of total number), Trans-Pecos (33%), and surrounding areas (17%). Given this large number of aoudad in areas where bighorn sheep are found, the potential for disease transmission and associated risks (e.g., epizootic hemorrhagic fevers, bluetongue, pneumonia, scrapie, and others; Candela et al., 2008; Cassman, Frese, & Greenlee, 2021; Fox, Muller, Spraker, Wood, & Miller, 2021; Hampy, Pence, & Simpson, 1979; Morawski, Carlson, Chang, & Johnson, 2013; Richomme, Gauthier, & Fromont, 2006) and competition between aoudad and bighorn sheep (Barrett, 1967; McCarty & Bailey, 1994; Seegmiller & Simpson, 1979; Simpson, Krysl, & Hampy, 1978) remains a high-priority management concern. Although aoudad are numerous in Texas, they are listed as ‘vulnerable’ in their native range by the IUCN Red List of Threatened Species (Cassinello et al., 2008). In fact, the number of non-native aoudad in the US are thought to outnumber those existing in the native range (Cassinello et al., 2008; Stipoljev et al., 2021). Based on zoo records, it appears that aoudad initially were imported into the New York Zoological Park and the National Zoological Park in the US, circa 1900 (Mungall & Sheffield, 1994; Ogren, 1959). Later, private ranches (William Randolph Hearst Ranch in California circa 1930 and Joe McKnight Ranch in New Mexico circa 1940) obtained progeny from various zoos across the US for viewing and hunting opportunities, which are commonly thought to be the source of free-ranging populations established in California and New Mexico (Barrett, 1980; Mungall & Sheffield, 1994; Ogren, 1965). In the 1950’s, state agencies (New Mexico Department of Game and Fish, NMDGF and Texas Parks and Wildlife Department, TPWD) translocated aoudad from the Hearst and McKnight ranches into northeastern New Mexico and the Panhandle of Texas, respectively (DeArment, 1971, Mungall & Sheffield, 1994; Ogren, 1965). Further, throughout the 1950s and 1970s, private ranches independently introduced aoudad (Simpson & Krysl, 1981) into the eastern, central, and southwestern portions of Texas (Mungall & Sheffield, 1994). It is unclear whether these translocations included individuals previously established in Texas or were products of additional importations from their native range, zoos, or introduced populations in Europe. At present, similar translocation efforts and population expansion continue with aoudad now being common throughout the western two-thirds of Texas. Currently, >30,000 free-ranging aoudad are estimated to occur in Texas; with most populations residing in the Trans-Pecos region, followed by the Edwards Plateau and Panhandle regions (F. Hernández, TPWD, personal communication; Traweek & Welk, 1992; Fig. 3); although aoudad occur in other ecoregions as a result of private introductions in high-fenced, non-free-ranging operations, and subsequent escapees (Schmidly & Bradley, 2016). Given that native desert bighorn sheep and exotic aoudad were reintroduced and introduced, respectively, in 1957, direct genetic comparisons of aoudad to desert bighorn sheep provides an opportunity to determine why aoudad populations are exponentially increasing in number and desert bighorn sheep populations continually struggle to survive. Conservation efforts are needed for both species as populations of desert bighorn sheep in Texas currently are experiencing a decline presumably as a result of disease events and aoudad are considered vulnerable in their native range of northern Africa. I employed two genetic sequencing methodologies: 1) traditional mitochondrial markers (cytochrome¬-b and displacement loop) to understand maternal lineages and 2) double digest Restriction-site Associated DNA Sequencing (RAD-seq) to discern differences within and between populations of desert bighorn sheep and aoudad.

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Aoudad, Ammotragus lervia, Bighorn Sheep, Conservation, Cytochrome-b gene, Displacement loop, Ovis canadensis, RAD-seq