In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex SANTIAGO S  ANCHEZ-RAM  IREZ,* † RODHAM E. TULLOSS, ‡ 1 LAURA GUZM  AN-D  AVALOS, § JOAQU  IN CIFUENTES-BLANCO, ¶ RICARDO VALENZUELA,** ARTURO ESTRADA-TORRES, †† FELIPE RU  AN-SOTO, ‡‡ RA  UL D  IAZ-MORENO, §§ NALLELY HERN  ANDEZ-RICO, ¶¶ MARIANO TORRES-G  OMEZ,*** HUGO LE  ON ††† and JEAN-MARC MONCALVO* † *Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON M5S 2C6, Canada, †Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON M5S 3B2, Canada, ‡P. O. Box 57, Roosevelt, NJ 08555-0057, USA, §Departamento de Botanica y Zoologıa, Universidad de Guadalajara, Zapopan 45101, Mexico, ¶Facultad de Ciencias, Departamento de Biologıa Comparada, UNAM, Ciudad Universitaria, Mexico City 04510, Mexico, **Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City 11340, Mexico, ††Centro de Investigacion en Ciencias Biologicas, Universidad Autonoma de Tlaxcala, Tlaxcala 90122, Mexico, ‡‡Facultad de Ciencias Biologicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutierrez 29039, Mexico, §§Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango 34120, Mexico, ¶¶Laboratorio de Etnobiologıa, Centro de Investigaciones Biologicas, Universidad Autonoma del Estado de Hidalgo, Pachuca, Mexico, ***Centro de Investigaciones en Ecosistemas CIEco, Antigua carretera a Patzcuaro # 8701, Col. Ex-Hacienda de San Jose de La Huerta, Morelia 58190, Mexico, †††Coleccion Etnomicologica “Dr. Teofilo Herrera Suarez”, Instituto Tecnologico del Valle de Oaxaca, Xoxocotlan 71230, Mexico Abstract 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 harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addi- tion, high extinction rates and genetic erosion are 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 specia- tion. Many of these dynamic processes and patterns can be inferred through phyloge- netic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Cae- sar’s mushrooms species complex) using multilocus 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 geographical sampling through- out 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 midrange 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 multispecies coalescent in compara- tive phylogeographical analyses and diversity assessments that include ancestral species. Correspondence: Santiago Sanchez-Ramırez, Fax: +1 416 586 8025; E-mails: santiago.snchez@gmail.com and santiago.sanchez@mail.utoronto.ca 1 Res. Assoc. (hons.), New York Botanical Garden, Bronx, NY, USA © 2015 John Wiley & Sons Ltd Molecular Ecology (2015) 24, 5938–5956 doi: 10.1111/mec.13413