Study area and samples

We analyzed DNA from 730 individual red foxes collected throughout the western U.S. between 1986 and 2018 (Table S1; Fig. ​Fig.1).1). For convenience, we refer to two broad regions of the study area: (1) the “Far West,” which includes the high-elevation Pacific ranges (Cascades, Sierra Nevada) and the low-elevation valley and coastal areas to their west, and (2) the “Intermountain West,” which includes the high-elevation Rocky Mountain and Great Basin ranges and the surrounding lower elevation, cold desert basins (i.e., the Columbia Plateau, the Snake River Plain, and the lower elevations of the Great Basin). Generally, the high-elevation mountain ranges encompass the historical distribution of indigenous western red foxes (Hall and Kelson 1959), whereas lower elevations correspond to either populations known to originate from fur farms (California; Sacks et al. 2016) or those of poorly characterized ancestry (cold desert basins; Fichter and Williams 1967; Verts and Carraway 1998; Kamler and Ballard 2003). The Sacramento Valley subspecies (V. v. patwin) is an exception to this elevational characterization, in that it is sister to the high-elevation Sierra Nevada subspecies but occupied the grassland-dominated Sacramento Valley prior to European colonization (Sacks et al. 2010; Volkmann et al. 2015).

Circles indicate the location of collection, with dark fill specifying those known from previous studies to be introduced via fur farms (Sacks et al. 2011, 2016). Colored polygons depict coarse historical ranges of native western subspecies according to Hall and Kelson (1959) and modified by the genetic findings of Sacks et al. (2010). Finer-scaled historical habitat associations are approximated by gray shading, which depicts a merged version of Kuchler’s (1964) vegetation categories, “conifer forest” and “alpine meadows or barren”. The Far West, referred to throughout the main text, includes red foxes in the Pacific mountains (Cascades, Sierra Nevada) and westward, whereas the Intermountain West includes red foxes in the Rocky Mountains and surrounding cold desert basins (Great Basin, Columbia Plateau, Snake River Plain).

Most of the 730 DNA samples were used in previous studies but typed at only a subset of the genetic markers used here (e.g., mitochondrial only; see Table S1 for details); 251 samples were newly collected. The majority (62%) of samples were tissue or blood collected opportunistically from mortalities (e.g., foxes killed via vehicle strikes), pelts with permission of trappers, or live captures for other studies whose trapping and handling methods followed American Society of Mammalogists animal care guidelines (Sikes et al. 2011) and were approved by the University of California, Davis Animal Care and Use Committee (IACUC No. 17860). From more remote montane regions, we additionally incorporated noninvasively collected hair and fecal samples (e.g., Hiller et al. 2015; Akins et al. 2018). Tissue and hair were stored in desiccant or frozen at −20 °C and fecal samples were stored in >95% ethanol. We extracted DNA from feces using QIAamp Stool Kit (Qiagen Inc., Valencia CA), and from hair, urine, and tissue using DNeasy Blood and Tissue Kits (Qiagen Inc.) using previously described protocols (e.g., Quinn et al. 2019).