PT  - JOURNAL ARTICLE
AU  - Jessica L. Allen
AU  - Sean K. McKenzie
AU  - Robin S. Sleith
AU  - S. Elizabeth Alter
TI  - First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure
AID  - 10.1101/237164
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 237164
4099  - http://biorxiv.org/content/early/2017/12/21/237164.short
4100  - http://biorxiv.org/content/early/2017/12/21/237164.full
AB  - Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics of Cetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested that C. linearis had a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns in C. linearis, and more broadly, in rare and endangered fungi.We would like to thank the following people for aiding with this research: Alex Cecil and Jenna Dorey for their field assistance, Gary Kauffman for help locating populations throughout the National Forest and many helpful discussions about Gymnoderma, Chris Ulrey for help locating the species on Blue Ridge National Park land, and especially for rapelling expertise, Dr. Richard Harris for conducting microscopy to search for trichogynes and spores. Library preparations and sequencing was conducted at The Rockefeller Genome Resource Center. Funding for this research came from Highlands Biological Station, NSF GRFP, and NSF DEB#1145511.