References

Allen, J., Calabria, L., Glew, K., Villella, J., & Dillman, K. (2021). Pseudocyphellaria rainierensis. Retrieved February 21, 2021, from http://iucn.ekoo.se/iucn/species_view/369711/

Allen, J. L., McKenzie, S. K., Sleith, R. S., & Alter, S. E. (2018). First genome‐wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. American Journal of Botany, 105(9), 1556-1567.

Allen, J. L., McMullin, R. T., Tripp, E. A., & Lendemer, J. C. (2019). Lichen conservation in North America: a review of current practices and research in Canada and the United States. Biodiversity and Conservation, 28(12), 3103-3138.

Allen, J. L., McMullin, R. T., Wiersma, Y. F., & Scheidegger, C. (2021). Population genetics and biogeography of the lungwort lichen in North America support distinct Eastern and Western gene pools. American Journal of Botany, 108(12), 2416-2424.

Alonso‐García, M., Grewe, F., Payette, S., & Villarreal A, J. C. (2021). Population genomics of a reindeer lichen species from North American lichen woodlands. American Journal of Botany, 108(1), 159-171.

Catchen, J., Hohenlohe, P., Bassham, S., Amores, A., and Cresko, W. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013

Devkota, S., Chaudhary, R. P., Werth, S., & Scheidegger, C. (2019). Genetic diversity and structure of the epiphytic foliose lichen Lobaria pindarensis in the Himalayas depends on elevation. Fungal Ecology, 41, 245-255.

Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020). RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences, 117(17), 9451-9457.

Glavich, D. A. (2013). Conservation Assessments for 5 species of Lichens. USDA Forest Service Region, 6.

Imshaug, H. A. (1950). New and noteworthy lichens from Mt. Rainier National Park. Mycologia, 42(6), 743-752.

Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405.

Kamvar, Z. N., Tabima, J. F., & Grünwald, N. J. (2013). Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction (No. e161v1). PeerJ PrePrints.

Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature biotechnology, 37(5), 540-546.

Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. bioinformatics, 25(14), 1754-1760.

Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing genomic data quality and beyond. Current Protocols, 1, e323. doi: 10.1002/cpz1.323

Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A. (2018). Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34: i142–i150.

McCune, B., & Geiser, L. (2009). Macrolichens of the Pacific Northwest. Oregon State University Press.

NatureServe (2022). Current Conservation Status for Pseudocyphellaria rainierensis. Retrieved July 11, 2022, from https://explorer.natureserve.org/Taxon/ELEMENT_GLOBAL.2.126647/Pseudocyphellaria_rainierensis.

Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290.

Pfeffer, B., Lymbery, C., Booth, B., & Allen, J. L. (2023). Chromosomal genome sequence assembly and mating-type (MAT) locus characterization of the leprose asexual lichenized fungus Lepraria neglecta (Nyl.) Erichsen. The Lichenologist, 55(1), 41-50.

Sillett SC, McCune B, Peck JE, Rambo TR, Ruchty A (2000) Dispersal limitations of epiphytic lichens result in species dependent on old-growth forests. Ecolog Appl 10:789–799

Smit, A. F. A., Hubley, R., & Green, P. (2016). RepeatMasker at http://repeatmasker. org. Nucleic Acids Res.

Tripp, E. A., Tsai, Y. H. E., Zhuang, Y., & Dexter, K. G. (2017). RAD seq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra‐arid deserts of Namibia. Ecology and Evolution, 7(19), 7920-7936.

Villella, J., Calabria, L., McCune, B., Miller, J. E., & Sharrett, S. (2022). An Annotated Checklist of Lichens of the Opal Creek Wilderness and Adjacent Areas: a Pre-Fire Baseline. (In Press)

Widhelm, T. J., Grewe, F., Huang, J. P., Ramanauskas, K., Mason‐Gamer, R., & Lumbsch, H. T. (2021). Using RADseq to understand the circum‐Antarctic distribution of a lichenized fungus, Pseudocyphellaria glabra. Journal of Biogeography, 48(1), 78-90.