Data from: In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex

Some of the effects of past climate dynamics on plant and animal diversity
make-up have been relatively well studied, but to less extent in fungi.
Pleistocene refugia are thought to harbor high biological diversity (i.e.
phylogenetic lineages and genetic diversity), mainly as a product of
increased reproductive isolation and allele conservation. In addition,
high extinction rates and genetic erosion is expected in previously
glaciated regions. Some of the consequences of past climate dynamics might
involve changes in range and population size that can result in divergence
and incipient or cryptic speciation. Many of these dynamic processes and
patterns can be inferred through phylogenetic and coalescent methods. In
this study, we first delimit species within a group of closely related
edible ectomycorrhizal Amanita from North America (the American
Caesar's mushrooms species complex) using multi-locus
coalescent-based approaches; and then address questions related to effects
of Pleistocene climate change on the diversity and genetics of the group.
Our study includes extensive geographic sampling throughout the
distribution range, and DNA sequences from three nuclear protein-coding
genes. Results reveal cryptic diversity and high speciation rates in
refugia. Population sizes and expansions seem to be larger at mid-range
latitudes (Mexican highlands and SE USA). Range shifts are proportional to
population size expansions, which were overall more common during the
Pleistocene. This study documents responses to past climate change in
fungi, and also highlights the applicability of the multi-species
coalescent in comparative phylogeographic analyses and diversity
assessments that include ancestral species.