Population genomics of a reindeer lichen species from North American lichen woodlands

Abstract

Lichens are one of the main structural components of plant communities in the North American boreal biome. They play a pivotal role in lichen woodlands, a large ecosystem situated north of the closed-crown forest zone, and south of the forest-tundra zone. In Eastern Canada (Quebec), there is a remnant LW found 500 km south of its usual distribution range, in the Parc National des Grands-Jardins, originated mainly because of wildfires. We inferred the origin of the lichen Cladonia stellaris from this LW and assessed its genetic diversity in a postfire succession. METHODS: We genotyped 122 individuals collected across a latitudinal gradient in Quebec. Using the software Stacks, we compared four different approaches of locus selection and single-nucleotide polymorphism calling. We identified the best fitting approach to investigate population structure and estimate genetic diversity of C. stellaris. RESULTS: Populations in southern Quebec are not genetically different from those of northern LWs. The species consists of at least four phylogenetic lineages with elevated levels of genetic diversity and low co-ancestry. In Parc National des Grands-Jardins, we reported high values of genetic diversity not related with time since fire disturbance and low genetic differentiation among populations with different fire histories. CONCLUSIONS: This first population genomic study of C. stellaris is an important step forward to understand the origin and biogeographic patterns of lichen woodlands in North America. Our findings also contribute to the understanding of the effect of postfire succession on the genetic structure of the species.

Species boundaries in the messy middle—A genome‐scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi

“…The raw reads from the MiSeq sequencing were processed and assembled Stacks v2.3 (Rochette et al, 2019 ) as described earlier for metagenomic datasets of lichens (Alonso‐García et al, 2021 ). In short, we demultiplexed reads of individuals from the pool of raw sequence reads based on their barcodes with the script “process‐radtags.” The demultiplexed reads of each individual were aligned to the reference genome database using Bowtie2 (Langmead & Salzberg, 2012 ).…”

“…Interpreting anatomical, chemical, and morphological characters of lichens within a phylogenetic framework has transformed our understanding of the role of phenotypic characters used for lichen‐forming fungal taxonomy (Printzen, 2010 ). While portions of the ribosomal cistron, including the internal transcribed spacer (ITS)—the standard barcoding marker for fungi (Schoch et al, 2012 ), and regions of the mitochondrial genome, have been the standard genetic loci for lichen fungi systematics, genomic data have become increasingly useful when studying closely related species or recently diverged populations (Allen et al, 2018 ; Alonso‐García et al, 2021 ; Grewe et al, 2017 ; Leavitt et al, 2016 ; Widhelm et al, 2021 ).…”

Genomic Resources for the First Federally Endangered Lichen: The Florida Perforate Cladonia (Cladonia perforata)

“…These findings contrast strongly with studies of widespread LFF. Cladonia stellaris, for instance, was found to lack spatial genetic structure across a very large geographic area in Quebec, Canada [54], and Alors et al [55] recovered a similar pattern in Parmelina carporrhizans. In a circum-Antarctic study of Pseudocyphellaria glabra, Widhelm et al [46] found evidence for clades that largely correspond to continental-level regions with few instances of intercontinental gene flow, thus showing some spatial structure, though on a very large spatial scale.…”