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Thesis (PhD (Botany and Zoology))--Stellenbosch University, 2008. / ENGLISH ABSTRACT: The worldwide movement of biota is of substantial concern for the conservation of biodiversity. The movement of species takes place at three different scales. These are translocations of indigenous species within their natural distribution ranges, the translocation of species outside their natural distribution ranges within geopolitical boundaries (i.e. extralimital introductions) and the translocation of species outside geopolitical boundaries and their natural distribution ranges (i.e. extraregional introductions). Ungulates are extensively translocated at each of these scales and each scale of translocation is expected to have different impacts on biodiversity. Ungulates are translocated for conservation purposes such as reintroducing species to places where they have previously gone extinct and to mitigate inbreeding in small, isolated populations. Ungulates are also extensively translocated for economic and recreational reasons, such as for sport hunting. Translocations for sport hunting include indigenous, extralimital and extraregional species. Concerns for translocations of indigenous species are largely for the loss of genetic diversity through the mixing of genetically distinct populations, and concerns for extralimital and extraregional translocations are for impacts on indigenous biodiversity such as through herbivory, competition, hybridization and disease transmission. This thesis investigates the extent of ungulate introductions globally and at a finer resolution in South Africa. It investigates the pathways, drivers and impacts of ungulate introductions and it also investigates the use of surrogates for genetic distinctiveness for advising the translocation of indigenous ungulates. The study finds that ungulate translocations have been extensive and have lead to the homogenization of ungulate assemblages in countries globally and at a quarter-degree grid-cell resolution in South Africa. Zoos were identified as a potential introduction pathway for extraregional ungulates globally and in South Africa extraregional introductions have made ungulate assemblages more different; whereas large numbers of extralimital introductions have made ungulate assemblages more similar. The homogenization of ungulate species in South Africa has increased with time, due to increased numbers of translocations, particularly of extralimital species. In South Africa translocations have most recently been made to high-income areas with high human population density and high livestock density; whereas in the 1960s ungulates were introduced to areas species poor for indigenous ungulates and marginal for livestock. In South Africa, long distance translocations of indigenous species extralimitally has resulted in extensive range expansions of a magnitude greater than predicted range changes as a result of predicted climate change. When the use of surrogates of genetic distinctiveness for advising translocations was investigated for Africa, the East African rift valley was found to be important in delineating genetic distinctiveness and translocations across this feature should be prevented. Major rivers in Africa also showed potential for delineating genetic distinctiveness in ungulates, but relevant phylogeographic data are needed to confirm this. Sufficient evidence for the impacts of non-indigenous ungulates on biodiversity both in South Africa and globally is lacking despite substantial concern for their impacts. It is suggested that to demonstrate the impacts of non-indigenous ungulates exclosure and enclosure experiments should be used and population declines in indigenous species should be shown. / AFRIKAANSE OPSOMMING: Verskuiwing van plante en diere wêreldwyd lei tot groot kommer in gevolge die bewaring van biodiversiteit. Verskuiwings vind op drie skale plaas, naamlik, die verskuiwing van inheemse spesies binne hulle natuurlike verspreidingsgebied, die verskuiwing van spesies buite hul natuurlike verspreidingsgebied maar binne landsgrense (d.w.s. buite limiet verskuiwings), en die verskuiwing van spesies buite hul natuurlike verspreidingsgebied en buite landsgrense (d.w.s. buite grondgebied verskuiwings). Grootskaalse verskuiwing van hoefdiere vind op al drie skale plaas. Verskuiwing op elk van die skale sal na verwagting biodiversiteit verskillend beïnvloed. Hoefdiere word ook vir bewaringsdoeleindes verskuif, bv. die herbevolking van ‘n gebied waar die spesies uitgesterf het, asook om genetiese probleme wat gepaardgaan met klein bevolkingsgroottes te vermy. Hoefdiere word ook verskuif vir ekonomiese- en ontspannings redes, o.a. vir sportjag, en sluit verskuiwings op al drie skale in. Kommer oor verskuiwings binne ‘n spesies se verspreidingsgebied rus hoofsaaklik op die verlies van genetiese diversiteit a.g.v. die vermenging van vorig genetiese eiensoortige bevolkings, terwyl op die ander twee skale kommer hoofsaaklik gebaseer is op die impakte van kompetisie, interteling, predasie, herbivoor effek, en die verspreiding van parasiete op inheemse biodiversiteit. Hierdie proefskrif ondersoek die omvang van hoefdier verskuiwings globaal asook in Suid Afrika. Die verskuiwingsweë, oorsake en impakte van verskuiwings word hier ondersoek, asook die maatstawwe van genetiese eiensoortigheid om advies oor verskuiwings te verskaf. Die bevindings toon op ekstensiewe verskuiwing van hoefdiere wat eenvormigheid van hoefdier spesiesamestellings wêreldwyd bevorder het, sowel as op ‘n kwartgraad skaal in Suid Afrika. Dieretuine is geïdentifiseer as ‘n potensiële bron van buite grondgebied verskuiwings. In Suid Afrika het buite grondgebied verskuiwings hoefdier spesiesamestellings minder eenvormig gemaak, terwyl buite limiet verskuiwings hoefdier samestellings binne Suid Afrika meer eenvormig gemaak het. Eenvormigheid in hoefdier spesiesamestellings het met tyd in Suid Afrika toegeneem as gevolg van ‘n toename in veral buite limiet verskuiwings. In Suid Afrika is verskuiwings mees onlangs na hoë-inkomste gebiede met hoë menslike bevolkingsen veëdigthede gemaak. In die sestiger jare is hoefdiere egter verskuif na gebiede waar min inheemse hoefdiere voorgekom het en wat marginaal was vir veëboerdery. In Suid Afrika het langafstand buite limiet verskuiwings versoorsaak dat die verspreidingsgebiede van sekere hoefdier spesies groter is as wat die geval sal wees met voorspelde klimaatsveranderinge. Waneer surogaat inligting gebruik word om genetiese verskille tussen bevolkings te identifiseer om verskuiwings te adviseer, word die Oos Afrika Rift vallei geïdentifiseer as ‘n belangrike breuk tussen bevolkings. Verskuiwings oor die vallei moet verkieslik nie plaasvind nie. Groot riviere in Afrika speel ‘n soortgelyke rol, maar verdere genetiese inligting is nodig om dit te bevestig. Alhoewel kommer oor die impak van verskuiwings groot en teoreties verdedigbaar is, bestaan daar te min konkrete bewyse vir die impakte in Suid Afrika. Daar word voorgestel dat manipuleringseksperimente uitgevoer moet word om impakte te demonstreer, en dat aandag veral gegee moet word aan die demonstrasie van impakte op inheemse spesies.

In Utah, farmers are concerned that ungulates are damaging safflower (Carthamus tinctorius) fields. I examined elk (Cervus elaphus) and mule deer (Odocoileus hemionus) damage to safflower production in San Juan County, Utah during 2009 and 2010. Data on damaged safflower plants were collected within 28 fields, totaling 1,581 ha (13 fields totaling 963 ha during 2009; 15 fields totaling 618 ha during 2010). I compared 3 methods to assess losses: ungulate-proof exclosures, adjacent plant compensation method, and counting the number of damaged plants in 50-m transects (safflower count method). Exclosures were of limited use because they could not be erected until farmers stopped using cultivating their fields. Hence, this method did not account for ungulate damage to young plants. The adjacent plant compensation method assessed yields within 1 m of a randomly-selected damaged plant to account for any compensatory growth of neighboring plants but this method proved inaccurate because ungulate herbivory was concentrated so that a browsed plant was often surrounded by other browsed plants so no compensatory growth by surrounding plants occurred. The most accurate method was the safflower count method which determined the number of damaged plants within a field and then multiplied this number by the decrease in yield from an average damaged plant. I used this method to examine 981,000 plants for damage. Deer and elk damaged or killed 7.2% of safflower plants during 2009 and 1.4% of plants during 2010. Overall yield reduction was 2.9% during 2009 and 0.6% in 2010. The total value of safflower loss within all surveyed fields in 2009 was $9,023 for a loss of $9.42 / ha. The loss of value within surveyed fields in 2010 was $2,330, or $3.77 / ha. The best model for predicting ungulate damage in 2009 included distance to canyon from field edge and the percent of a field bordered by a fallow field, while the best model for 2010 included distance to canyon from field edge and the percent of a field bordered by a wheat field. Safflower farmers were surveyed in the spring of 2010 to compare perceived losses in their fields during 2009 to those measured in this study. Farmers believed that damage by deer and elk reduced their yields by 20% with most damage caused by elk (x¯ =12% by elk, 7% by deer, 1% by other wildlife). On average, perceptions of damage were 5.2 times higher than the actual levels I measured during 2009. This was not surprising because farmers usually surveyed their field from the field’s edge and ungulate damage was concentrated along the edge of the fields.

Mutualisms are delicately balanced partnerships and are increasingly recognized as being fundamental to patterns and processes within ecological systems. Changes to the ecological setting in which such interactions operate can disrupt this balance. By understanding the context-dependent nature of such associations, researchers can begin to understand how changes in the environment can have cascading effects on the entire community within which they occur. Oxpeckers (Buphagus spp.) feed on the ectoparasites of ungulates in sub-Saharan Africa and from the blood of ungulate wounds. Because of this dichotomy in feeding behavior, the role of oxpeckers as consistently beneficial partners of their hosts has been questioned, and it has been suggested that the concept of conditional mutualism be applied to this interaction. I combined observational studies of oxpeckers in Kruger National Park, South Africa, with experiments on oxpeckers in captivity at the Mokopane Biodiversity Conservation Centre, South Africa, to test the hypothesis that the ectoparasite cleaning service provided by oxpeckers to their hosts is context-dependent. The results of my dissertation research demonstrate that the oxpecker-ungulate association has conditional outcomes. Under certain conditions, the oxpecker-ungulate relationship is a nutritional mutualism where ungulates provide food (ticks) for oxpeckers in exchange for a cleaning service. Under other conditions, oxpeckers exploit their hosts to feed from their blood. My findings suggest that a high abundance of the tick species and tick stages oxpeckers prefer is necessary to maintaining an alignment of interests between oxpeckers and ungulates. When ungulates host few ticks of the species oxpeckers prefer, these birds will wound-feed to meet their nutritional demands. Such wound-feeding threatens the balance of the oxpecker-ungulate mutualism. Although oxpeckers frequently wound-fed in captivity, the frequency of wound-feeding events on wild host species was only 3.1% of feeding events. Whether the relationship between oxpeckers and domesticated hosts differs from that between oxpeckers and wild hosts, or if this observed difference is actually a result of researcher constraints in the wild, needs further exploration.

Population dynamics of large ungulates are complex and vary with fluctuations in factors such as predation, resource availability, human disturbance, and weather (Gaillard et al. 1998, Forrester and Wittmer 2013). These regulating factors exhibit similar effects on ungulate populations by changing vital rates such as birthrate, death rate, emigration or immigration (Gaillard et al. 2000). To better understand the mechanisms influencing population change, it is useful to involve tools from multiple disciplines (Krausman et al. 2013). Here we explore population dynamics of mule deer (Odocoileus hemionus) through the lenses of two distinct fields: population ecology and genomics. In the first chapter we examine the influence of maternal effects on offspring fitness. In the second chapter we present a high-quality, chromosome-level reference genome for mule deer. We expect results from each of these studies to provide valuable resources for continued research and conservation of mule deer.

I studied the characteristics of fence mortality in pronghorn (Antilocapra americana), mule deer (Odocoileus hemionus), and elk (Cervus elaphus) along roads in Colorado and Utah from June 2004 to June 2005. I defined a direct-fence mortality as a carcass caught directly in a fence and an indirect-fence mortality as a carcass on the ground within 10 m of a fence. I estimated an average annual direct mortality occurrence of 0.25 mortalities/km (0.078 mule deer mortalities/km, 0.113 pronghorn mortalities/km, and 0.061 elk mortalities/km). The highest fence-mortality rates for ungulates occurred during August, which coincided with weaning of fawns on my study area. Mule deer and pronghorn both jumped fences in >81% of observed crossings and did not differ in their crossing methods (P = 0.37). Getting caught between the top 2 wires was the leading cause of death for fence mortalities. Mule deer suffered higher fence-mortality rates than elk or pronghorn because they crossed fences more frequently and fed in the right-of-way of the road more often (P < 0.001). Juveniles were 8 times more likely to die in fences than adults. Woven-wire fence types were more lethal to ungulates (especially juveniles) than other fence types (P < 0.001). Woven wire with a single strand of barbed wire above it was significantly more lethal to ungulates than woven wire with 2 strands of barbed wire above it, or 4-strand barbed-wire fence (P < 0.001). There was a direct relationship between the frequency of fence-mortalities and ungulate abundance (P < 0.001 ). Traffic volumes had an inverse relationship with fence mortality frequencies (P < 0.001) and ungulate densities along the right-of-way (P < 0.001). Indirect mortality (i.e., carcasses within 10 m of fences) composed 66% of fence-related mortality, whereas direct-fence mortality (i.e., carcasses in fences) composed a mere 33%. Additionally, indirect-fence mortality was found to be greater along woven-wire fences, when compared to barbed-wire fence types (P = 0.003).

Foraging decisions of large herbivores can be affected by many factors and have great effect on both above- and below-ground ecosystems. Here, I determine to which degree temporal (seasonality), or spatial (habitat) factors influence the foraging behaviour of Svalbard reindeer (Rangifer tarandus platyrhynchus) and asses if small-scale foraging behaviour correlates with an animals’ patch residence time. I analysed behavioural observations on 15 Svalbard reindeer between summer and autumn 2022, recording both behaviour and habitat use. Using mixed-effects multinomial logistic regression, the interaction between seasonal change from summer to autumn and habitat best explained the variation in Svalbard reindeer foraging behaviour. The foraging behaviour “standing-grazing” was found to have the highest observed amount in all habitat types and increased over the growing season. Contrastingly, the foraging behaviour of “walking-grazing” had its highest abundance in the beginning of the study period, and then decreased over the course of the season for all analysed habitats. In addition, “walking-grazing” was found to be significantly correlated with patch residency time and decreased the longer an individual stayed in a patch. With presumable high plant quality early in the season, my results imply how Svalbard reindeer are greatly stationary foragers, but prioritizing to become relatively mobile when it is beneficial. Thus, highlighting how Svalbard reindeer respond dynamically to shifts in foraging conditions. These findings provide knowledge about what factors may impact the foraging behaviours of Arctic herbivores and helps contribute to a broader understanding of how changes in foraging behaviours may alter arctic ecosystems.

<p>White-tailed deer (Odocoileus virginianus; hereafter deer) are a keystone herbivore within forest ecosystems. While deer rely on plant species for growth, reproduction, and survival, multiple external factors can dictate browsing behavior. These factors ultimately drive browsing selection, browsing intensity, and diet composition, which in turn can shape the influence deer have on forest ecosystems. To better understand the complex relationship between deer populations, their habitat, and public perception of deer, the Indiana Department of Natural Resources partnered with Purdue University to initiate the Integrated Deer Management Project (IDMP). As part of the IDMP, this dissertation evaluated the ecological condition of deer habitat to assess the influence deer have on woody and herbaceous plant species within Indiana forests. Our study aimed to i) rank woody species according to their selection by deer and evaluate how the ranking of individual species varies across the state (Chapter 2); ii) evaluate variables and spatial extents associated with differences in browsing intensity, and evaluate different indices used to assess differences in browsing intensity (Chapter 3); iii) quantify winter deer diet composition using DNA barcoding to evaluate how diets vary across a gradient of deer densities, browsing intensities, non-native plant densities, and landscape characteristics (Chapter 4); and iv) evaluate the interactive effects of deer, non-native plant species, and landscape characteristics on the herbaceous layer of forests, while further evaluating the spatial extent at which landscape characteristics are most strongly related to herbaceous-layer composition and diversity (Chapter 5). To do this, I sampled 152 woodlots over three years across three regions of Indiana, collecting data on the browsing selection of individual woody species, the browsing intensities on all woody species, and the composition of vegetation communities (Chapters 2, 3, and 5, respectively). To address diet composition (Chapter 4), we collected deer pellet groups to analyzed diet components. We ranked a total of 63 woody species regarding their browsing selection by deer. While most of these remained consistent from region to region, 16 varied greatly in selection, as deer often showed increased selection for a given species when it resided in an area that provided greater browsing opportunities. Browsing intensity was most associated with food availability, however, it was also influenced by deer density in the region with the lowest forest cover. The twig age index of browsing intensity showed promise as the most efficient and effective index for use in Indiana woodlots. Although diet composition did not differ across regions of Indiana, we found 16 that deer consumed several uncommon taxa when the greater landscape exhibited homogenous patch composition. Similarly, deer consumed different native taxa in forested landscapes with greater deer densities in comparison to agricultural landscapes with lower deer densities. Lastly, though browsing varied within and across regions landscape characteristic, and not deer, were the most influential suite of variables. Additionally, the spatial extent at which these variables exhibited their best fit varied depending on the dependent variable being evaluated and the region of analysis. Together, our results highlight that variables ranging from the woodlot to the landscape-scale influence browsing behavior. This showcases that deer respond to variables at varying scales when browsing and in general, browse more in areas that offer the greatest benefit, whether these areas offer greater food availability or quality, or offer lower risks associated with anthropogenic development. This suggests that when managing forests for deer both woodlot and landscape context should play a role in the decision process. Although differences in browsing were observed, deer had less impact on the herbaceous layer compared to other variables we examined. This suggests that, in contemporary forests, landscape characteristics may be the drivers of changes, and species composition may reflect a long-term history of deer herbivory with less variability resulting from differences in contemporary deer abundance within and across regions.  </p>

Mule deer (Odocoileus hemionus) are an ecologically, economically, and socially important species across much of the western United States. As such, populations and habitat are intensely managed by state game agencies. However, populations have been declining in recent decades and several factors have been implicated (e.g., climate, predation, competition, and habitat availability). Population dynamics of mule deer are driven by a combination of survival of adults and juveniles and reproductive rates. While adult female mule deer typically have consistently high annual survival rates (85% annually), juveniles are more easily affected by stressors (biotic and abiotic conditions) and therefore their annual survival rates are generally low and highly variable. In an effort to better understand the effects of management on—and the habitat needs for—reproduction and recruitment, we examined the potential effects of male-biased harvest on recruitment in populations of mule deer and the selection of sites for parturition by mule deer females. Changes in buck:doe ratio due to male-biased harvest may alter rates of pregnancy, timing of parturition, and synchrony of parturition if inadequate numbers of males are present to fertilize females during their first estrous cycle. If rates of pregnancy or timing of parturition are influenced by decreased buck:doe ratios, recruitment may be reduced. This results from fewer births, later parturition (resulting in lower survival of fawns), and a less synchronous parturition period (increasing the proportion of neonates exposed to predation). Our objectives were to compare rates of pregnancy, timing of parturition, and synchrony of parturition between exploited populations of mule deer with relatively high (Piceance Basin) and relatively low (Monroe Mountain) buck:doe ratios. We determined rates of pregnancy via ultrasonography and timing of parturition via expulsion of vaginal implant transmitters. We found no differences in rates of pregnancy, timing of parturition, or synchrony of parturition between Monroe Mountain and Piceance Basin. This suggests that the relatively low buck:doe ratios typical of heavily harvested populations do not have unintended or indirect impacts on population dynamics because recruitment remains unaffected. Because neonate ungulates are most vulnerable to predation during parturition and shortly thereafter, selecting sites for parturition can have direct fitness consequences. We investigated the selection of sites for parturition by mule deer. We utilized vaginal implant transmitters to identify sites of parturition. We then obtained and compared macro- and micro-habitat features between sites of parturition and associated random sites. Parturitient females selected sites based on topography, habitat-type, and obscurity. Enhanced understanding of habitat variables that are selected for parturition provides insight into the life history or behavior of a species and allows managers to ensure that suitable habitat is available for this stage of life-cycles.

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