title: In and out of refugia: historical patterns of diversity and demography in the North American Caesar's mushroom species complex.
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 addition, 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 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 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 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 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 comparative phylogeographical analyses and diversity assessments that include ancestral species.
authors.affiliation: 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.
authors.forename: Santiago
authors.initials: S
authors.lastname: Sánchez-Ramírez
authors.affiliation: P. O. Box 57, Roosevelt, NJ, 08555-0057, USA.
authors.forename: Rodham E
authors.initials: RE
authors.lastname: Tulloss
authors.affiliation: Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan, 45101, México.
authors.forename: Laura
authors.initials: L
authors.lastname: Guzmán-Dávalos
authors.affiliation: Facultad de Ciencias, Departamento de Biología Comparada, UNAM, Ciudad Universitaria, México City, 04510, México.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Cifuentes-Blanco
authors.affiliation: Escuela Nacional de Ciencias Biólogicas, Instituto Politécnico Nacional, México City, 11340, México.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Valenzuela
authors.affiliation: Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, 90122, México.
authors.forename: Arturo
authors.initials: A
authors.lastname: Estrada-Torres
authors.affiliation: Facultad de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, 29039, Mexico.
authors.forename: Felipe
authors.initials: F
authors.lastname: Ruán-Soto
authors.affiliation: Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, 34120, México.
authors.forename: Raúl
authors.initials: R
authors.lastname: Díaz-Moreno
authors.affiliation: Laboratorio de Etnobiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Hidalgo, Pachuca, México.
authors.forename: Nallely
authors.initials: N
authors.lastname: Hernández-Rico
authors.affiliation: Centro de Investigaciones en Ecosistemas CIEco, Antigua carretera a Pátzcuaro # 8701, Col. Ex-Hacienda de San José de La Huerta, Morelia, 58190, México.
authors.forename: Mariano
authors.initials: M
authors.lastname: Torres-Gómez
authors.affiliation: Coleccion Etnomicológica "Dr. Teófilo Herrera Suárez", Instituto Tecnológico del Valle de Oaxaca, Xoxocotlán, 71230, México.
authors.forename: Hugo
authors.initials: H
authors.lastname: León
authors.affiliation: 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.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Moncalvo
mesh_terms: D000545:Amanita / Q000145:classification* / Q000235:genetics; D001499:Bayes Theorem; D005075:Biological Evolution; D057231:Climate Change; D004271:DNA, Fungal / Q000235:genetics; D005800:Genes, Fungal; D005828:Genetics, Population; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques; D009656:North America; D010802:Phylogeny; D058974:Phylogeography; D011156:Population Density; D000068236:Refugium; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal
keywords: *BEAST; BP&P; Plio-Pleistocene; ancestral area reconstruction; cryptic diversity; diversification; edible ectomycorrhizal fungi; species delimitation