Genomic Architecture, Ecological Differentiation, and Genetic Diversification of Manzanitas
Manzanitas (Arctostaphylos, Ericaceae) are shrub species found in the California Floristic Province (CFP), a biodiversity hotspot of western North America. These plants are adapted to the summer dry period and fire disturbance of the CFP, and form the most diverse woody genus in the CFP flora. Among over 100 currently recognized manzanita species and subspecies, many are considered rare and endangered. The current understanding of manzanita adaptation and diversification is poor, limiting our ability to carry out ecological, evolutionary, and conservation studies on these plants. A comprehensive understanding of genomic composition can advance knowledge of the genetic basis underlying the fire- and drought adaptation of manzanitas. We annotated the first manzanita genome assembly to provide genomic resources for downstream studies of adaptation and diversification. Our analyses indicate that our manzanita genome is well-assembled and annotated. It is enriched with terpenoid genes, which may play essential roles in the fire and drought adaptations of manzanitas. Understanding the ecological diversification of manzanitas can benefit the identification of species with distinct habitats and help researchers to derive effective conservation strategies. We used machine learning algorithms to conduct a quantitative study of niche differentiation among manzanita species. Although we did not identify any species with habitat distinctiveness within the genus, we determined that soil and climatic data can distinguish some species from other species in the same geographic region. Next-generation sequencing data can provide invaluable insight into species and subspecies boundaries, and facilitate the identification of taxa with unique genotypes that require conservation attention. We applied reduced-representation genomic sequencing technology to test the hypothesis that Eastwood Manzanita (Arctostaphylos glandulosa) subspecies are genetically differentiated. We observe that genetic structure within Eastwood manzanita does not correspond to current subspecies circumscriptions, but rather reflects geographic distribution. In addition, only one of two subspecies of conservation concern appeared to be genetically distinct. Our findings that resulted from these genomic, genetic, and ecological studies advance our knowledge of manzanita adaptation and diversification and form the basis for better conservation strategies for these important species.