Date of Degree


Document Type


Degree Name





James Lendemer

Committee Members

Christopher Blair

Elizabeth Alter

Jessica Allen

Yoshihito Ohmura

Subject Categories

Botany | Genetics | Genomics | Other Ecology and Evolutionary Biology


Ascomycota, Cladoniaceae, homing endonluclease genes, species delimitation, next-generation sequencing, North America


The genus Cladonia represents one of the most speciose genera of lichenized fungi, with more than 500 known species encompassing a diverse array of morphologies and habits. These lichens form keystone species in many habitats, serving a variety of ecological roles. However, despite being among of the more well studied lichens, there is much still unknown or under-studied about them. As is the case with most lichen study systems, phylogenetic study has been limited to a small number of partial loci, while adoption of next-generation sequence methods has been slow. As a consequence, there are still knowledge gaps in Cladonia phylogenetics and comparative genomics. The limited application of molecular data has also left most species, even iconic and well-known taxa such as C. rangiferina, without an effective re-assessment of species boundaries with molecular data. Like all lichens, Cladonia species are also understudied in terms of conservation, with only a handful of the speciose genus assessed with IUCN Red List guidelines. In this dissertation, I take steps in addressing some of these current shortcomings over five studies; i) I review and analyze the application of traditional sequence data and the adoption of next-generation sequence data in lichens since 2000, ii) I conduct a population survey and IUCN Red List assessment for a geographically restricted and overlooked species, C. submitis, listing the species as Endangered (EN), iii) I sequence and assemble the mitochondrial genomes of multiple Cladonia species and examine the mitochondrial genome architecture and diversity of homing endonuclease genes within and among species in the genus, iv) I assess the evolutionary relationships and species boundaries of three morphologically similar and partly co-occurring species, C. rangiferina, C. oricola and C. stygia, and v) I investigate the delimitation between widely disjunct populations of C. submitis, describe the population in east Asia as C. miyabii sp. nov., and assess the species as Vulnerable (VU) under IUCN guidelines. These studies generated a wealth of assembled mitochondrial genomes and other molecular data for Cladonia, provided the first intraspecific comparison of lichen mitochondrial genomes and homing endonuclease genes, established molecular support for multiple distinct species including one new to science, and contributed to a steadily growing body of conservation assessments, of which lichens are desperately in need.