Genetic analyses of increasing power are now regularly incorporated into wildlife management assessments of threatened and endangered species. Genetic data provide valuable information regarding taxonomy, kinship, and population size and structure. Recently transformed by the advent of powerful technologies that expand our view from single genes to the entire genome, the field of conservation may be on the verge of another revolution with the emergence of epigenetics as a promising means of surveying environmental response in natural populations. In this dissertation, I present my doctoral research upon population genetics and epigenetics of pronghorn (Antilocapra americana). Considerable effort has been undertaken to conserve pronghorn, particularly in the periphery of its range in the southwestern United States and northwestern Mexico. Translocation is regularly used to supplement and re-establish populations of the wide-ranging A. a. americana subspecies while captive breeding has been established for two endangered pronghorn subspecies, A. a. sonoriensis found in Arizona and Sonora, Mexico and A. a. peninsularis of the Baja Peninsula. The primary goal of my doctoral work was to provide pronghorn managers with current estimates of genetic diversity, relatedness, and structure within and between pronghorn subspecies in the desert southwest. My work shows that conservation measures for A. a. sonoriensis have successfully maintained genetic diversity within this endangered subspecies. My estimates of population structure within A. a. americana in northern Arizona reveal the influence of translocation and habitat fragmentation and demonstrate the successful reestablishment of gene flow following the removal of highway fences. With the purpose of guiding future release of captive pronghorn, I explored the subspecies status of pronghorn extirpated from a portion of their range in southern California and northern Baja California. My analyses of museum specimens indicate that the historical range of A. a. peninsularis may have extended as far north as the international border while specimens collected just north of the border share more genetic identity with A. a. sonoriensis. To follow my interests in epigenetics, I also conducted the first ever conservation epigenetics study with Arizona pronghorn. I found that pronghorn are more epigenetically than genetically diverse and this is an indicator that further epigenetic study will reveal the signature of response to environmental factors, as it has with other species demonstrating this pattern.

When a species is introduced outside their native range, the genetic diversity of the introduced population is generally decreased due to the founder effect, and the fitness of individuals in the introduced population may decrease due to inbreeding depression. Invasive species are a paradox to this paradigm because while the initial population size of an invasive species may be small in their non-native range, the individuals are able to survive, eat, and reproduce so successfully, that they have deleterious effects on native species. One mechanism that invasive species use to overcome a lack of genetic diversity and adapt to their new environment is CpG methylation, a heritable and environmentally influenced epigenetic modification that regulates the expression of certain genes to alter phenotypes without altering an organism’s DNA sequence.Bighead and silver carps, two species of bigheaded carp native to eastern Asia, are believed to have been introduced to the United States in the 1970s. Since that time, populations of both bighead and silver carp have surged, particularly in the Mississippi River drainage, where they compete with native planktivores for food, injure boaters, and threaten the multi-million dollar fisheries industry in the Great Lakes. In this study, methylation-sensitive amplified fragment length polymorphisms (MS-AFLPs) were used to analyze the genetic and epigenetic diversity of bighead and silver carp from the Gan, Pearl, and Yangtze rivers in their native China and from the Illinois River in the United States. While the heterozygosity of silver carp in Illinois was not found to be significantly lower than that of silver carp in China, the silver carp in Illinois did show a significantly higher level of methylation compared to Chinese silver carp. There is evidence that CpG methylation may play a significant role in allowing silver carp to adapt and thrive in an introduced environment.

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