Syst. Biol. 65(5):824–842, 2016 © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syw055 Advance Access publication June 10, 2016 Spatiotemporal Diversification of the True Frogs (Genus Rana): A Historical Framework for a Widely Studied Group of Model Organisms , ZHI-Y ONG YUAN1 2,WEI-WEI ZHOU1,XIN CHEN3,NIKOLAY A. POYARKOV,JR.4,HONG-MAN CHEN1, NIAN-HONG JANG-LIAW5,WEN-HAO CHOU6,NICHOLAS J. MATZKE7,KOJI IIZUKA8,MI-SOOK MIN9, ,∗ ,∗ ,∗ ,∗ SERGIUS L. KUZMIN10,YA-PING ZHANG1 ,DAV I D C. CANNATELLA11 ,DAV I D M. HILLIS11 , AND JING CHE1 1State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan; 2Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan; 3Department of Biological Sciences, Dartmouth College, Hanover, HN 03755, USA; 4Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskiye Gory, GSP-1, Moscow 119991, Russia; 5Animal Department, Taipei Zoo, 30 6 Xinguang Road, Sec. 2, Taipei 11656, Taiwan; Department of Zoology, National Museum of Natural Science, 1st Kuang-Chien Road, Taichung 40453, Downloaded from Taiwan; 7Division of Ecology, Evolution, and Genetics, Research School of Biology, The Australian National University, ACT 2601, Australia; 8Kanda-Hitotsubashi JH School, 2-16-14 Hitotsubashi, Chiyoda-ku, Tokyo 101-0003, Japan; 9Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 151-742 Seoul, South Korea; 10 Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119234, Russia; and 11 Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA ∗ Correspondence to be sent to: Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan or http://sysbio.oxfordjournals.org/ Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA E-mail: [email protected], [email protected], catfi[email protected], [email protected] The first three authors share equal first authorship. Received 19 September 2015; reviews returned 11 December 2015; accepted 31 May 2015 Associate Editor: Richard Glor Abstract.—True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to at University of Texas Austin on August 26, 2016 clarify the group’s diversification and global biogeography. Our analyses consistently support an “Out of Asia” pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29–18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci. [Amphibians; biogeography; diversification rate; Holarctic; transcontinental dispersal.] Biodiversity is distributed heterogeneously across of early, rapid cladogenesis followed by a slowdown Earth. Consequently, the determinants of spatial in diversification rate is thought to be related to patterns of diversity are of paramount interest ecological constraints (Schluter 2001; Rabosky 2009). for biologists (Gaston 2000; Ricklefs 2004). Broadly Further, increases in cladogenesis are often associated distributed, species-rich clades provide an opportunity with broad-scale environmental changes or geological to explore the evolutionary processes that drive diversity processes (e.g., orogenesis). across large spatiotemporal scales (e.g., Derryberry et al. Diverse clades that are distributed across several 2011; McGuire et al. 2014). Methods combining the major continental areas provide excellent opportunities dynamics of diversification (e.g., speciation, extinction) to compare patterns of distribution and diversification with biogeographic history allow biologists to test in different regions (Qian and Ricklefs 2000; McGuire hypotheses of diversification within and between et al. 2014). In this article we investigate the spatial regions (Ricklefs 2004; Wiens and Donoghue 2004; and temporal patterns of regional and continental-scale Mittelbach et al. 2007). biodiversity in a widely studied clade that is broadly If speciation and extinction rates (ignoring dispersal distributed across Eurasia and the Americas, the true for the moment) are roughly constant across geographic frogs (genus Rana, sensu AmphibiaWeb 2015). areas, then species diversity is influenced by time- True frogs are extensively used as model organisms in dependent processes (McPeek and Brown 2007). studies of development, genetics, physiology, behavior, However, changes in speciation rate (e.g., by adaptive ecology, and evolution (see Duellman and Trueb 1986). radiations) or extinction rate (e.g., by climate effects) The first successful laboratory cloning experiment of can quickly disrupt the correlation between clade age an animal (transfer of a nucleus into an enucleated and species diversity. In many radiations, a pattern egg, resulting in a normal organism) was conducted 824 2016 YUAN ET AL.—SPATIOTEMPORAL DIVERSIFICATION OF THE TRUE FROGS 825 in Rana pipiens (Briggs and King 1952), and various The family Ranidae began to diversify about 57 Ma species of Rana continue to be used widely in studies (Bossuyt et al. 2006; Wiens et al. 2009), long after the of physiology and genetics. Many species of Rana are breakup of Pangaea (>120 Ma, Sanmartín et al. 2001). also commonly studied in the field as well as the Therefore, the global distribution of the family must laboratory. One of the most extensive monographs have resulted from intercontinental dispersal. Based on on the ecology and life history of an amphibian was limited sampling of Rana, Bossuyt et al. (2006) suggested based on Rana temporaria (Savage 1962), and studies that the ancestor(s) of the American Rana reached the of Rana ecology, behavior, conservation, and evolution New World in one or two waves from Eurasia, without have accelerated in recent years (reviewed by Hillis and specifying the route of dispersal. Macey et al. (2006) Wilcox 2005). suggested two alternative hypotheses: two dispersals More than 100 described species of Rana from Asia to America via Beringia, or one dispersal from (AmphibiaWeb 2015) range across Europe (12 species) Asia to America with a second back-dispersal to Asia. We and Asia (32 species), and from North America to asked the following questions: the northern half of South America (57, plus several Downloaded from recognized but not yet described species; Hillis and (1) When did the intercontinental dispersal of Rana Wilcox 2005). Species occur in a wide variety of occur between Eurasia and the Americas? Were habitats including tundra, temperate coniferous and these dispersals via trans-Atlantic land bridges deciduous forests, grasslands, deserts, brackish-water (Case 1978) or by trans-Beringian (Pacific) land bridges (Macey et al. 2006)? Was there only one marshes, freshwater streams and lakes, montane http://sysbio.oxfordjournals.org/ cascades, semitropical cloud forests, and tropical dispersal from Eurasia to the Americas, with rainforests (Hillis and Wilcox 2005). Many species a dispersal back to Eurasia, or were there two are of conservation concern, and several species are distinct dispersal events into the New World? recently extinct or threatened with extinction. Despite When did major dispersal events within Eurasia the diversity of the genus and its importance in many and the Americas occur (e.g., into Europe, and into biological investigations, no comprehensive analysis of the Neotropics)? the spatial patterns and drivers of diversity for Rana has been published. (2) To what extent was dispersal into new areas The Eurasian species are morphologically accompanied by increased diversification rates? conservative. They possess prominent dorsolateral Were speciation rates highest when a lineage at University of Texas Austin on August 26, 2016 folds, a dark temporal mask, and a body that is entered new regions, or were they relatively countershaded in various shades of brown, leading to constant? the common English name “brown frogs” (Boulenger (3) How did geologic