University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Navy Research U.S. Department of Defense 2016 Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis) W. Chris Funk Robert E. Lovich Paul A. Hohenlohe Courtney A. Hofman Scott A. Morrison See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usnavyresearch This Article is brought to you for free and open access by the U.S. Department of Defense at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in U.S. Navy Research by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors W. Chris Funk, Robert E. Lovich, Paul A. Hohenlohe, Courtney A. Hofman, Scott A. Morrison, T. Scott Sillett, Cameron K. Ghalambor, Jesus E. Maldonado, Torben C. Rick, Mitch D. Day, Nicholas R. Polato, Sarah W. Fitzpatrick, Timothy J. Coonan, Kevin R. Crooks, Adam Dillon, David K. Garcelon, Julie L. King, Christina L. Boser, Nicholas Gould, and William F. Andelt Molecular Ecology (2016) 25, 2176–2194 doi: 10.1111/mec.13605 Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis) W. CHRIS FUNK,* ROBERT E. LOVICH,† PAUL A. HOHENLOHE,‡ COURTNEY A. HOFMAN,§¶** SCOTT A. MORRISON,†† T. SCOTT SILLETT,‡‡ CAMERON K. GHALAMBOR,* JESUS E. MALDONADO,**§§ TORBEN C. RICK,¶ MITCH D. DAY,‡ NICHOLAS R. POLATO,¶¶ SARAH W. FITZPATRICK,*** TIMOTHY J. COONAN,††† KEVIN R. CROOKS,‡‡‡ ADAM DILLON,‡‡‡ DAVID K. GARCELON,§§§ JULIE L. KING,¶¶¶ CHRISTINA L. BOSER,†† NICHOLAS GOULD**** and WILLIAM F. ANDELT‡‡‡ *Department of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA, †Naval Facilities Engineering Command Southwest, 1220 Pacific Highway, San Diego, CA 92132, USA, ‡Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA, §Department of Anthropology, University of Maryland, College Park, MD 20742, USA, ¶Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA, **Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA, ††The Nature Conservancy, San Francisco, CA 94105, USA, ‡‡Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013-7012, USA, §§Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA, ¶¶Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA, ***Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA, †††National Park Service, Channel Islands National Park, 1901 Spinnaker Drive, Ventura, CA 93001, USA, ‡‡‡Department of Fish, Wildlife and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO 80523, USA, §§§Institute for Wildlife Studies, P.O. Box 1104, Arcata, CA 95518, USA, ¶¶¶Catalina Island Conservancy, P.O. Box 2739, Avalon, CA 90704, USA, ****Fisheries, Wildlife and Conservation Biology, North Carolina State University, Turner House, Box 7646, Raleigh, NC 27695-7646, USA Abstract The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are pre- dicted to be strong on islands and both could drive population divergence and specia- tion. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Chan- nel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mech- anism driving population divergence among island fox populations. In particular, pop- N = – ulations had exceptionally low genetic variation, small e (range 2.1 89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests Correspondence: W. Chris Funk, Fax: +1 970 491 3289; E-mail: [email protected] © 2016 John Wiley & Sons Ltd POPULATION DIVERGENCE IN THE ISLAND FOX 2177 – F identified 3.6 6.6% of loci as high ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity F among populations based on high ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low N genetic variation and small e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. Keywords: conservation genomics, divergent selection, effective population size, genetic drift, population divergence Received 15 May 2015; revision received 17 February 2016; accepted 23 February 2016 manent reduction in genetic variation (or at least a long- Introduction term reduction, as mutation may eventually partially Islands are global centres of biodiversity and endemism replenish lost genetic variation; Eldridge et al. 1999). (Stuart et al. 2012), but the evolutionary mechanisms Divergent selection is also expected to be strong generating this diversity are typically poorly under- among island populations due to high environmental stood (with some notable exceptions, e.g., Losos et al. heterogeneity among islands and between islands and 1998; Grant & Grant 2002; Jordan & Snell 2008). Isola- the mainland (Weigelt et al. 2013). One potential source tion is a common feature associated with divergence of environmental variation on islands is climate, includ- and speciation among island populations (Grant 1998), ing temperature, precipitation and fog (Fischer & Still but ultimately, the processes of genetic drift and/or 2007). The specific position of islands relative to ocean divergent selection acting on standing genetic variation currents can have profound effects on their climate and new mutations is required for differences to accu- (Spalding et al. 2007), as do differences in elevation and mulate (Fisher 1930; Wright 1931, 1951). To date, most topography. Another source of environmental variation research on island biodiversity has largely focused on among islands is community composition. Island bio- those examples where divergent selection has generated geography theory makes the simple but important pre- striking cases of adaptive evolution (Losos et al. 1998; diction that larger islands have more species Grant & Grant 2002). However, much less attention has (MacArthur & Wilson 1967), but even adjacent islands been given to the role of genetic drift in generating dif- that are the same size may have different species due to ferences among isolated islands (Jordan & Snell 2008). climate, microhabitat availability, and random chance of Thus, investigating the joint roles of genetic drift and which species end up on which islands (Burns 2007). divergent selection is key for understanding how island Thus, both genetic drift and divergent selection can be populations diverge, thereby generating island biodiver- strong in island populations, which means either or sity and endemism. both processes could drive genetic differentiation and Genetic drift is expected to be strong in island popula- population divergence among islands. However, if drift tions for several reasons. First, many island populations is strong, it may overwhelm selection, precluding adap- are founded by a small number of individuals whose tive divergence (Wright 1931, 1951). genetic composition may differ significantly from the One of the most iconic island species in the world is source (often continental) population due to random the island fox (Urocyon littoralis), a species whose origin, chance (Martınez-Solano & Lawson 2009; Kolbe et al. evolution and divergence has fascinated evolutionary 2012). Second, island populations often have small effec- biologists for decades (Grinnell et al. 1937; Gilbert et al. tive population sizes (Ne). Especially if an island is lim- 1990; Wayne et al. 1991; Collins 1993; Goldstein et al. ited in size, it may have a low carrying capacity and, as 1999; Aguilar et al. 2004). This species is a diminutive, a result, a small Ne (Frankham 1998; Eldridge et al. endemic fox sister to the mainland grey fox (Urocyon 1999). The third reason is bottlenecks. Like many popu- cinereoargenteus) and is found on six of the eight Chan- lations, island populations are likely to experience fluc- nel Islands off the coast of southern California (Fig. 1) tuations in population size in the course of