The field of bioinformatics began late in the 20th century to enable the analysis of proteomic, genetic, and genomic datasets. Since the 1990s and the advent of 'big data', there has been a glut of genomic data, and a dearth of people with the skillsets to analyze them. As of 2019, the world’s largest genetic sequence archive, NCBI's Short-Read Archive, was home to over 40 petabytes of genetic data, and that number is growing larger every day. Hidden within those sequences of As, Cs, Ts, and Gs, are the answers to many biological questions, including those pertaining to how we may best conserve species in the face of the existential threat of a drastically changing climate. One such species is the Warm Springs pupfish, which is endemic to several low-flow springs in the Ash Meadows National Wildlife Refuge in Southwestern Nevada. One population, at South Scruggs Spring, was facing a demographic collapse due to predation by invasive species, declining spring flow, and what may have been an extinction vortex. An extinction vortex is caused when inbreeding in small populations leads to the accumulation of deleterious genotypes, which causes low fecundity, feeding back into the low population size. Once a species enters into one, there is little we know of outside of human-facilitated introgression of novel genetic material that can save the population from extirpation. In 2009, ten individuals from a neighboring spring were added to South Scruggs and the population demographics were monitored over the following three years using mark-recapture combined with microsatellite genotyping. Based on the probability of recapture, I calculated that hybrid offspring of the ten introgressed individuals had a probability of survival between mark/recapture events that was 20% higher than that of the genetically poor resident individuals. In the process of the study, I sequenced and assembled the nuclear and mitochondrial genomes of the Warm Springs pupfish, which are resources that may be used to monitor the health of these isolated populations of endangered fish. Another class of organisms that is especially sensitive to changing environmental conditions are lichens, which are visually stunning symbiotic assemblages of a fungus, or mycobiont, and at least one photosynthetic partner, called the photobiont. Their genomes are relatively small, enabling a low cost of sequencing the genomes of both partners in the symbiosis. I was able to sequence and assemble the genomes of over 500 lichen specimens. Many of the mitochondrial genomes of these species were assembled, annotated, and published on NCBI as a result of this study. One of the primary resources to come from these sequences is a formidable database of molecular barcoding sequences–the ribosomal DNA complexes of over 400 of the different lichen species assemblies came together. Using this database, I developed a novel bioinformatic pipeline that was able to detect which lichen propagules are present in environmental metagenomic samples. Such a tool should enable researchers to evaluate factors leading to the ability of a lichen to establish in an area, versus which ones are only able to disperse into it, but not establish. In addition to the fungal rDNA complexes, algal rDNA complexes also assembled. By aligning metagenomic reads to these algal and cyanobacterial complexes, I was able to calculate the diversity of the photobiont communities within each lichen thallus and test the conditions determining photobiont diversity. I concluded that algal photobiont diversity is highest in the surface-adhering crustose lichens, and lowest in the tufty, three-dimensional fruticose lichens. In lichens that use cyanobacteria as their photobiont, diversity decreases with elevation. Surprisingly, and contrary to our expectations, lichen photobiont diversity did not differ between sexual and asexual species. The bioinformatic pipelines and data sets generated in this thesis provide valuable information on understudied and threatened species. These resources will enable adjacent researchers to make better decisions about conservation of these species in the face of habitat loss, pollution, and a changing climate.</p
