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1 April 2012 Microsatellite analysis of raccoon (Procyon lotor) population structure across an extensive metropolitan landscape
Trenten T. Santonastaso, Jean Dubach, Stephanie A. Hauver, William H. Graser, Stanley D. Gehrt
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Understanding population structure can lend insight into the spread of animal-borne disease, and the effects of anthropogenic land use on habitat. Raccoons are highly adaptive to human land development and can persist in a wide range of habitat types, making them ideal subjects for investigating the level of population structure in a highly fragmented area. A total of 323 raccoons were livetrapped from 7 locations encompassing 3 distinct habitat types (agriculture, urban forest preserves, and residential) across the Chicago metropolitan region (maximum distance between 2 sites was 128 km). Genetic analyses of 14 microsatellite loci indicate that although raccoon populations across the region share up to 50% of the allelic diversity, they segregated into at least 2 distinct subpopulations, dividing the Chicago metropolitan region into northern and southern groups with further structure occurring within these larger groups. Incorporating sample sites between the identified north–south groups may provide greater resolution as to where this split occurs. Although there is evidence of population structure between all sample sites, migrant analysis suggests there is enough gene flow to preserve genetic diversity throughout the population.

Habitat fragmentation via anthropogenic activity such as road building and land development continues to impact mesopredator populations to varying degrees (Crooks 2002; Ditchkoff et al. 2006; Prange et al. 2003; Riley et al. 2006). Understanding how population structure, dispersal, and social behaviors change in response to habitat alterations can serve to illustrate the extent of human impact on natural systems. Although traditional field studies are critical to understanding a species, it can be difficult to obtain comprehensive data for nocturnal, arboreal, and forest-dwelling animals (Cullingham et al. 2008). However, as molecular techniques such as microsatellite genotyping have been developed and extended over the past 25 years, collecting data for cryptic species has become possible. Associated with those technologies, sophisticated statistical methods have been developed to determine gene flow within and among populations (Christian and George 2008; Molenberghs 2005). This information can be used to infer population structure and individual behavior with greater fidelity, even with animals that are difficult to observe.

Raccoons (Procyon lotor) in the Chicago area are ideal candidates for a molecular population study of their ecology, which will aid in the understanding of an important reservoir of zoonotic pathogens in the urban environment. Raccoons are abundant throughout the Chicago area, which is highly fragmented by both natural and artificial barriers. The Chicago River bisects the region, and there are at least 9 interstate highways, 6 United States highways, and 15 state highways that cut through the area. Habitat fragmentation also occurs through land alteration for agriculture, industry, and housing. Because raccoons are highly adaptable (Crooks 2002; Cullingham et al. 2008), they can be observed in nearly all habitat types that occur within the highly fragmented landscape of the Chicago area (Prange et al. 2004; Randa and Yunger 2006). Although their ubiquitous distribution from rural to urbanized sites suggests that they successfully disperse throughout their range, studies of other mid- to large-sized carnivores show that habitat fragmentation can hinder movement. For example, vehicular traffic associated with a single highway has been shown to reduce gene flow in coyotes (Canis latrans), bobcats (Lynx rufus), and grizzly bears (Ursus arctos horribilisMillions and Swanson 2007; Proctor et al. 2002; Riley et al. 2006; Sacks et al. 2004).

Raccoon population structure and dispersal patterns can influence the way a zoonotic disease moves through a landscape. In an area with human populations, those patterns can have significant impacts on human health. Raccoons are host to dozens of pathogenic agents that are communicable to humans (leptospirosis, roundworm, and rabies) and other animals (canine distemper, pneumonia, and rabies) alike (Page et al. 2008; Rosatte et al. 2010). These highly adaptable animals often exploit human structures and trash for shelter and food (Bozek et al. 2007; Prange et al. 2004), increasing their densities in urban forest preserves and residential neighborhoods (Graser 2008; Prange et al. 2003). Such increased densities of wild animals are often correlated with epizootics and an increased risk to human health (Page et al. 2005; Riley et al. 1998).

Raccoons from the Midwest have been the subject of many field studies over the past 15 years (e.g., Hauver et al. 2010; Prange et al. 2004; Stevens et al. 1995). Nevertheless, few have examined the effects of urbanization on raccoons over large distances, and none have used genetic tests on this scale. Because raccoons are habitat generalists, they make an ideal model species on which to study epizootics in a fragmented environment. Understanding gene flow across a large region provides valuable insight as to how disease will travel through a population (Recuenco et al. 2008; Rees et al. 2009; Rosatte et al. 2006). This study specifically addresses the following questions: Are raccoons in the Chicago area panmictic, or is there hidden population structure? Does habitat size or habitat type affect genetic parameters? This study represents a key component to understanding the ecological role raccoons play in a highly developed region.

Materials and Methods

Study area

Rush Creek (RC