UCLA

In small isolated populations the fate of mutations is governed largely by chance rather than natural selection. Most mutations are deleterious, thus the inability of selection to effectively eradicate them incurs a cost to the genetic health of individuals in small populations. These detrimental consequences have been observed in numerous captive and wild populations, such as the gray wolves (Canis lupus) of Isle Royale, which suffer from severe inbreeding depression. However, other small populations appear healthy, and even persist for thousands of generations, such as the foxes (Urocyon littoralis) of the Channel Islands near the coast of Southern California. In this dissertation, we explore the genome-wide effects of small population size and isolation in these two extreme examples. First, we show that long-term small population size and isolation has led to a striking lack of diversity in island foxes, particularly in San Nicolas foxes, which are virtually monomorphic across the entire genome. Additionally, island foxes have an elevated burden of deleterious mutations relative to mainland gray foxes (U. cinereoargenteus), but show no signs of inbreeding depression. Second, we explore the possibility that strongly deleterious recessive alleles have been purged from island fox populations, facilitating their persistence, and allowing them to recover rapidly from extreme bottlenecks. We found that recent, short-term bottlenecks have had little impact on island fox genomes, and confirm through simulations that island populations are expected to have a reduced burden of strongly deleterious recessive alleles relative to mainland foxes. In contrast, Isle Royale wolves suffer from severe inbreeding depression, and are on the verge of extinction less than a century after the population was founded. Third, we show through whole genome sequencing of Isle Royale wolves that intense inbreeding has eliminated variation in large genomic segments, causing the increased homozygosity of deleterious mutations. Our results suggest that persistence is possible in small populations large enough for selection to purge strongly deleterious recessive alleles without causing extinction, although the long-term effects of the elevated burden of weakly deleterious alleles and the loss of diversity in these small populations are difficult to predict.