Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore.

Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.

A landscape-scale framework to identify refugia from multiple stressors.

From a conservation perspective, quantifying potential refugial capacity has been predominantly focused on climate refugia, which is critical for maintaining the persistence of species and ecosystems. However, protection from other stressors, such as human-induced changes in fire and hydrology, that cause habitat loss, degradation, and fragmentation is also necessary to ensure that conservation efforts focused on climate are not undermined by other threats. Thus, conceptual and methodological advances for quantifying potential refugia from multiple anthropogenic stressors are important to support conservation efforts. We devised a new conceptual approach, the domains of refugia, for assessing refugial capacity that identifies areas where exposure to multiple stressors is low. In our framework, patterns of environmental variability (e.g., increased frequency of warm summers), thresholds of resilience, and extent and intensity of stressors are used to identify areas of potential refugia from a suite of ongoing anthropogenic stressors (e.g., changes in fire regime). To demonstrate its utility, we applied the framework to a Southern California landscape. Sites with high refugial capacity (super-refugia sites) had on average 30% fewer extremely warm summers, 20% fewer fire events, 10% less exposure to altered river channels and riparian areas, and 50% fewer recreational trails than the surrounding landscape. Our results suggest that super-refugia sites (∼8200 km2 ) for some natural communities are underrepresented in the existing protected area network, a finding that can inform efforts to expand protected areas. Our case study highlights how considering exposure to multiple stressors can inform planning and practice to conserve biodiversity in a changing world.

Marco Conceptual a para Identificar Refugios de Múltiples Amenazas a Escala de Paisaje Resumen Desde la perspectiva de la conservación, la cuantificación de la capacidad potencial de refugio se ha enfocado principalmente en los refugios climáticos, los cuales son críticos para mantener la persistencia de las especies y los ecosistemas. Sin embargo, la protección ante otros factores estresantes, como los cambios inducidos por los humanos en los incendios y la hidrología, que causan la pérdida, degradación y fragmentación del hábitat, también son necesarios para asegurar que los esfuerzos de conservación enfocados en el clima no sean afectados por otras amenazas. Por lo tanto, los avances conceptuales y metodológicos para cuantificar los refugios potenciales ante múltiples factores estresantes causados por el humano son importantes para asegurar que los esfuerzos de conservación logren sus objetivos. Diseñamos una nueva estrategia conceptual, los dominios de los refugios, para evaluar la capacidad de refugio de un paisaje donde la exposición a múltiples factores estresantes es baja. En nuestro marco conceptual usamos los patrones de variabilidad ambiental (p. ej.: incremento en la frecuencia de veranos cálidos), los umbrales de resiliencia y la extensión e intensidad de los factores estresantes para identificar las áreas de refugios potenciales a partir de un conjunto de factores antropogénicos persistentes (p. ej.: cambios en el régimen de incendios). Para demostrar su utilidad, aplicamos el marco conceptual a un paisaje del sur de California. Los sitios con una alta capacidad de refugio (sitios de súper-refugios) tuvieron en promedio un 30% menos veranos extremadamente cálidos, 20% menos eventos de incendios y 50% menos senderos recreativos que el paisaje circundante. Nuestros resultados sugieren que los sitios de súper-refugios (∼ 8,200 km2 ) para algunas comunidades naturales están subrepresentados en la red existente de áreas protegidas, un resultado que puede orientar los esfuerzos por expandir las áreas protegidas. Nuestro estudio de caso resalta que considerar la exposición a múltiples amenazas puede guiar la planificación y la práctica de la conservación de la biodiversidad en un mundo cambiante.

Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development.

Urban development has major impacts on connectivity among wildlife populations and is thus likely an important factor shaping pathogen transmission in wildlife. However, most investigations of wildlife diseases in urban areas focus on prevalence and infection risk rather than potential effects of urbanization on transmission itself. Feline immunodeficiency virus (FIV) is a directly transmitted retrovirus that infects many felid species and can be used as a model for studying pathogen transmission at landscape scales. We investigated phylogenetic relationships among FIV isolates sampled from five bobcat (Lynx rufus) populations in coastal southern California that appear isolated due to major highways and dense urban development. Divergence dates among FIV phylogenetic lineages in several cases reflected historical urban growth and construction of major highways. We found strong FIV phylogeographic structure among three host populations north-west of Los Angeles, largely coincident with host genetic structure. In contrast, relatively little FIV phylogeographic structure existed among two genetically distinct host populations south-east of Los Angeles. Rates of FIV transfer among host populations did not vary significantly, with the lack of phylogenetic structure south-east of Los Angeles unlikely to reflect frequent contemporary transmission among populations. Our results indicate that major barriers to host gene flow can also act as barriers to pathogen spread, suggesting potentially reduced susceptibility of fragmented populations to novel directly transmitted pathogens. Infrequent exchange of FIV among host populations suggests that populations would best be managed as distinct units in the event of a severe disease outbreak. Phylogeographic inference of pathogen transmission is useful for estimating the ability of geographic barriers to constrain disease spread and can provide insights into contemporary and historical drivers of host population connectivity.

Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and interpopulation spatial scales.

Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.