LETTER Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic Andrew Storfer, 1 * Michael E. Alfaro, 1 Benjamin J. Ridenhour, 1 James K. Jancovich, 2 Stephen G. Mech, 1,3 Matthew J. Parris 4 and James P. Collins 5 1 School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA 2 Molecular and Cellular Biology Program, School of Life Sciences, The BioDesign Institute, Arizona State University, Tempe, AZ 85287- 4601, USA 3 Biology Department, Albright College, Reading, PA 19612- 5234, USA 4 Department of Biology, University of Memphis, Memphis, TN 38152, USA 5 School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA *Correspondence: E-mail: astorfer@wsu.edu Abstract Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intra- specific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection. Keywords Ambystoma tigrinum, Ambystoma tigrinum virus, amphibian declines, emerging diseases, phylogenetic concordance, virulence. Ecology Letters (2007) 10: 1075–1083 INTRODUCTION Emerging infectious diseases are widely recognized as a threat to public health and are increasingly appreciated as having major effects on biological communities (McCallum & Dobson 1995). In some cases, pathogens can even cause host extinctions (DeCastro & Bolker 2005). Emerging pathogens are either recently introduced to new regions or naı ¨ve hosts, or are already endemic but have increased in impact because of environmental changes or genetic changes in the host or pathogen (Daszak et al. 2000). Distinguishing whether emerging infectious diseases are novel or endemic is critical because each scenario necessi- tates different avenues for further research and possible mitigation strategies. In the case of emerging endemic pathogens, research may focus on identification and mitigation of possible environmental cofactors or assessing whether recent genetic changes increased pathogen viru- lence or decreased host resistance (Daszak et al. 2000; Jancovich et al. 2005; Rachowicz et al. 2005). In the novel pathogen case, research may focus on reasons for spread, such as: pathogen host switching, recent introductions of infected hosts to new areas, or pathogen range expansion. Efforts may then focus on identifying the source localities or species and controlling spread, such as for sudden acute respiratory syndrome (SARS; Li et al. 2005). However, distinguishing between the novel vs. endemic hypotheses is difficult for any pathogen and has thus rarely been accomplished because of difficulties gathering adequate data to identify the source of the pathogen, molecular information to disentangle the geographic relationships of pathogen strains, and dating the age of the pathogen (Rachowicz et al. 2005). One way to determine whether pathogens are novel or endemic is to assess the extent to which they are coevolved with their host. Analyses of phylogenetic Ecology Letters, (2007) 10: 1075–1083 doi: 10.1111/j.1461-0248.2007.01102.x Ó 2007 Blackwell Publishing Ltd/CNRS