Document Type



Doctor of Philosophy



Date of Defense


Graduate Advisor

Robert E. Ricklefs


Nathan Muchhala


Robert J. Marquis

Nathan Muchhala

Scott Mangan

Jonathan Myers

Ivan Jimenez


Rare species are susceptible to extinction due to ecological and genetic factors. Understanding the distribution, ecology, and evolution of rare species can provide useful information for effective conservation. To investigate species rarity, this dissertation focuses on a species-rich and ecologically diverse genus, Quercus (oaks). In Chapter 1, I aimed to understand how interactions between hosts and soil microbes contribute to habitat restriction in oak species. I performed a soil inoculum experiment on two pairs of sister oak species that show habitat divergence. I found that host-specific soil microbes contribute to habitat divergence and exclusion among sister species of oaks, but habitat-specific microbes do not. In Chapter 2, I investigated how the amount of suitable habitat and range filling determine the interspecific variation in species range size among oaks. Using data of 183 oak species from the Americas, I found that range filling explained more variation in species range extent than the amount of suitable habitat did, suggesting that historical events, such as the Last Glacial Maximum, are critical to explain current species ranges. In Chapter 3 and Chapter 4, I studied the species delimitation and the maintenance of species boundaries in a putative endemic species, Quercus acerifolia (maple-leaf oak). In Chapter 3, I found that Q. acerifolia is morphologically distinct from the co-occurring close relatives, Q. shumardii and Q. rubra. However, I detected a collection bias that results in spuriously large morphological distinctions among species in herbarium specimens. I also found a high mismatch between species taxonomy and normally distributed morphological clusters. In Chapter 4, population genetic analyses and phylogenetic analyses, based on genome-wide SNPs, revealed that Q. acerifolia is likely a nascent species that recently diverged from Q. shumardii. While I detected gene flow from Q. shumardii and Q. rubra to Q. acerifolia, I found that the genetic integrity of Q. acerifolia is safeguarded by ecological selection related to harsh environments on dry and rocky mountain ridges. Collectively, my findings illustrate that the integration of ecological experiments, biogeographic analyses, and morphometric and genomic tools provides an in-depth understanding of species rarity, and can guide our decision-making for species conservation.