Urbanization impacts apex predator gene flow but not genetic diversity across an urban‐rural divide

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms (SNPs) were genotyped using double‐digest, restriction site‐associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome‐scale markers to document subtle impacts of urbanization on a wide‐ranging carnivore living near a large urban center.     

Parasite genetic differentiation by habitat type and host species: molecular epidemiology of Schistosoma japonicum in hilly and marshland areas of Anhui Province, China

Schistosoma japonicum , a parasite of significant public health importance in parts of China and Southeast Asia, is a true generalist pathogen with over 40 species of mammals suspected as definitive host reservoirs. In order to characterize levels of parasite gene flow across host species and identify the most important zoonotic reservoirs, S. japonicum larvae (miracidia) were sampled from a range of definitive host species in two contrasting habitat types within Anhui Province, China: a low-lying marshland region, and a hilly region, where animal reservoir populations may be predicted to differ substantially. Miracidia samples were genotyped using seven multiplexed microsatellite markers. Hierarchical F -statistics and clustering analyses revealed substantial geographical structuring of S. japonicum populations within Anhui, with strong parasite genetic differentiation between habitat types. Within most villages, there was very little or no parasite genetic differentiation among host species, suggesting frequent S. japonicum gene flow, and thus also transmission, across species. Moreover, the data provide novel molecular evidence that rodents and dogs are potentially very important infection reservoirs in hilly regions, in contrast to bovines in the marshland regions. The parasite genetic differentiation between habitat types might therefore be associated with contrasting host reservoirs. The high levels of parasite gene flow observed across host species in sympatric areas have important implications for S. japonicum control, particularly in hilly regions where control of infection among wild rodent populations could be challenging.     

Fractured Genetic Connectivity Threatens a Southern California Puma (Puma concolor) Population

Pumas (Puma concolor; also known as mountain lions and cougars) in southern California live among a burgeoning human population of roughly 20 million people. Yet little is known of the consequences of attendant habitat loss and fragmentation, and human-caused puma mortality to puma population viability and genetic diversity. We examined genetic status of pumas in coastal mountains within the Peninsular Ranges south of Los Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana Mountains are bounded by urbanization to the west, north, and east, and are separated from the eastern Peninsular Ranges to the southeast by a ten lane interstate highway (I-15). We analyzed DNA samples from 97 pumas sampled between 2001 and 2012. Genotypic data for forty-six microsatellite loci revealed that pumas sampled in the Santa Ana Mountains (n = 42) displayed lower genetic diversity than pumas from nearly every other region in California tested (n = 257), including those living in the Peninsular Ranges immediately to the east across I-15 (n = 55). Santa Ana Mountains pumas had high average pairwise relatedness, high individual internal relatedness, a low estimated effective population size, and strong evidence of a bottleneck and isolation from other populations in California. These and ecological findings provide clear evidence that Santa Ana Mountains pumas have been experiencing genetic impacts related to barriers to gene flow, and are a warning signal to wildlife managers and land use planners that mitigation efforts will be needed to stem further genetic and demographic decay in the Santa Ana Mountains puma population.     

Fine scale population genetic structure of pumas in the Intermountain West

In this study, I examined the population genetic structure of subpopulations of pumas (Puma concolor) in Idaho and surrounding states. Patterns of genetic diversity, population structure, levels of inbreeding, and the relationship between genetic differentiation and dispersal distance within and between 15 subpopulations of pumas were compared. Spatial analyses revealed that the Snake River plain was an important barrier to movement between northern and southern regions of Idaho. In addition, subpopulations south of the Snake River plain exhibited lower levels of genetic diversity, higher levels of inbreeding, and a stronger pattern of isolation by distance relative to subpopulations north of the Snake River plain. Lower levels of diversity and restricted gene flow are likely the result of historically lower population sizes in conjunction with more recent changes in habitat use and available dispersal corridors for movement. The subdivision of puma populations north and south of the Snake River plain, along with the patterns of genetic diversity within regions, indicate that landscape features are affecting the population genetic structure of pumas in Idaho. These results indicate that information about the effects of landscape features on the distribution of genetic diversity should be considered when designing plans for the management and conservation of pumas.     

Gene flow connects coastal populations of a habitat specialist,the Clapper Rail Rallus crepitans

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographical range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of the USA, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks and a weak pattern of genetic differentiation that increased with geographical distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the Atlantic coast of the USA, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioural factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.     

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.     

Genetic structure of American black bears in the desert southwest of North America: conservation implications for recolonization

American black bears (Ursus americanus) have recolonized parts of their former range in the Trans-Pecos region of western Texas after a >40-year absence. Assessment of genetic variation, structuring, gene flow, and dispersal among bear populations along the borderlands of Mexico and Texas is important to gain a better understanding of recolonization by large carnivores. We evaluated aspects of genetic diversity and gene flow for 6 sampling areas of black bears in southwestern North America using genotypic data from 7 microsatellite loci. Our results indicated that genetic diversity generally was high in the metapopulation of black bears in northern Mexico and western Texas. The episodic gene flow occurring via desert corridors between populations in northern Mexico and those in western Texas has permitted the establishment of only moderate levels of genetic structuring. Bayesian clustering analyses and assignment testing depicted the presence of 3 subpopulations among our 6 sampling areas and attested to the generally panmictic nature of bear populations in the borderlands region. The potentially ephemeral nature of the small populations in western Texas and genotypic characteristics of bears recolonizing these habitats attest to the importance of linkages along this portion of the borderlands of the United States and Mexico to effectively conserve and manage the species in this part of its range.     

Patterns of genetic structuring in a brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis> L.) metapopulation

One main challenge in conservation biology is to preserve genetic variability and adaptive variation within and among populations. However, constant anthropogenic habitat modifications have severe effects on the evolutionary dynamics shaping wild populations and pose a serious threat to the natural evolution of biodiversity. The aim of the present study was to unravel the genetic structuring of brown trout (Salmo trutta) populations in the largest freshwater catchment in Ireland, whose habitats have experienced major human-mediated changes over at least two centuries. A total of 419 juvenile fish were sampled from nine main rivers in the Corrib catchment and were genotyped using 12 microsatellites. Both Bayesian clustering and F _ST-based analyses of genetic variance sorted these populations into five main genetically distinct groups, characterized by different extent of genetic differentiation among populations. These groups were also characterized by some degree of admixture, which can be partly explained by recent gene flow. Overall, the study suggests that the Corrib trout may conform to a metapopulation model with local populations that show different degrees of isolation and are interconnected by various level of gene flow. Results add further insights into metapopulation evolutionary dynamics and provide a useful basis to implement appropriate conservation strategies.     

Spatial risk assessment of livestock exposure to pumas in Patagonia, Argentina

Livestock predation and associated human-carnivore conflicts are increasing worldwide and require the development of methods and concepts for risk assessment and conflict management. Here we use knowledge on habitat preference and distribution of pumas and provide a first assessment of the spatial risk of livestock to puma depredation in Patagonian ranches, Argentina. In an initial step, we developed a rule-based habitat model in a Geographic Information System (GIS) to predict the distribution of puma habitat at a regional scale in Patagonia. We then used empirically derived puma occurrence records from Patagonian ranches 1) to test our regional habitat predictions, and 2) to evaluate if paddock characteristics (vegetation cover, topography, and distance to roads) contribute to explain puma occurrences within ranches. Finally, we simulated three livestock management scenarios differing in their spatial and seasonal allocation of livestock to paddocks, and compared the likelihood of livestock exposure to pumas among scenarios. At a regional scale, 22% of the study region was predicted to be suitable for puma home ranges. The greatest uncertainty in these predictions resulted from assumptions on woody vegetation cover requirements at the home range scale. Within ranches, puma occurrences were positively associated with paddock topography, woody vegetation cover on paddocks, and proximity to predicted regional puma habitat. Comparing the risk of predation by puma among simulated livestock management scenarios implied that rotating livestock during seasons may help to reduce the likelihood of livestock exposure to pumas. Our results show the usefulness of rule-based habitat models for describing broad-scale carnivore distributions and for aiding risk assessments to mitigate conflicts between predators and human activities.     

Population genetic structure of rock ptarmigan in the 'sky islands' of French Pyrenees: implications for conservation

Expected consequences of global warming include habitat reduction in many cool climate species. Rock ptarmigan is a Holarctic grouse that inhabits arctic and alpine tundra. In Europe, the Pyrenean ptarmigan inhabits the southern edge of the species' range and since the last glacial maximum its habitat has been severely fragmented and is restricted to high-alpine zones or 'sky islands'. A recent study of rock ptarmigan population genetic in Europe found that the Pyrenean ptarmigan had very low genetic diversity compared with that found in the Alps and Scandinavia. Habitat fragmentation and reduced genetic diversity raises concerns about the viability of ptarmigan populations in the Pyrenees. However, information on population structuring and gene flow across the Pyrenees, which is essential for designing a sound management plan, is absent. In this study, we use seven microsatellites and mitochondrial control region sequences to investigate genetic variation and differentiation among five localities across the Pyrenees. Our analyses reveal the presence of genetic differentiation among all five localities and a significant isolation-by-distance effect that is likely the result of short dispersal distances and high natal and breeding philopatry of Pyrenean ptarmigan coupled with severe habitat fragmentation. Furthermore, analysis of molecular variance, principal component analysis and Bayesian analysis of genetic structuring identified the greatest amount of differentiation between the eastern and main parts of the Pyrenean chain separated by the Sègre Valley. Our data also show that the Canigou massif may host an isolated population and requires special conservation attention. We propose a management plan which includes the translocation of birds. If a sky island structure affects genetic divergence in rock ptarmigan, it may also affect the genetic structure of other sky island species having low dispersal abilities.     

Genetic Differentiation Among Populations of the Roseate Spoonbill (Platalea ajaja; Aves: Pelecaniformes) in Three Brazilian Wetlands

Effective population size, levels of genetic diversity, gene flow, and genetic structuring were assessed in 205 colonial Roseate spoonbills from 11 breeding colonies from north, central west, and south Brazil. Colonies and regions exhibited similar moderate levels of diversity at five microsatellite loci (mean expected heterozygosity range 0.50–0.62; allelic richness range 3.17–3.21). The central west region had the highest Ne (59). F _ST values revealed low but significant genetic structuring among colonies within the north and within the south regions. Significant global genetic structuring was found between the northern and central western populations as well as between the northern and southern populations. An individual-based Bayesian clustering method inferred three population clusters. Assignment tests correctly allocated up to 64% of individuals to their source regions. Collectively, results revealed complex demographic dynamics, with ongoing gene flow on a local scale, but genetic differentiation on a broader scale. Populations in the three regions may all be conserved, but special concern should be given to central western ones, which can significantly contribute to the species’ gene pool in Brazil.     

Landscape heterogeneity predicts gene flow in a widespread polymorphic bumble bee, Bombus bifarius (Hymenoptera: Apidae)

Bombus bifarius is a widespread bumble bee that occurs in montane regions of western North America. This species has several major color pattern polymorphisms and shows evidence of genetic structuring among regional populations, and the taxonomic status of regional populations has repeatedly been debated. We test whether observed structure is evidence for discrete gene flow barriers that might indicate isolation or instead reflects clinal variation associated with spatially limited dispersal in a complex landscape. We first consider color pattern variation and identify geographical patterns of B. bifarius color variation using cluster analysis. We then use climate data and a comprehensive set of B. bifarius natural history records with an existing genetic data set to model the distribution of environmentally suitable habitat in western North America and predict pathways of potential gene flow using circuit theory. Resistance distances among populations that incorporate environmental suitability information predict patterns of genetic structure much better than geographic distance or Bayesian clustering alone. Results suggest that there may not be barriers to gene flow warranting further taxonomic considerations, but rather that the arrangement of suitable habitat at broad scales limits dispersal sufficiently to explain observed levels of population differentiation in B. bifarius.     

Translocations maintain genetic diversity and increase connectivity in sea otters,Enhydra lutris

Sea otters, Enhydra lutris, were once abundant along the nearshore areas of the North Pacific. The international maritime fur trade that ended in 1911 left 13 small remnant populations with low genetic diversity. Subsequent translocations into previously occupied habitat resulted in several reintroduced populations along the coast of North America. We sampled sea otters between 2008 and 2011 throughout much of their current range and used 19 nuclear microsatellite markers to evaluate genetic diversity, population structure, and connectivity between remnant and reintroduced populations. Average genetic diversity within populations was similar: observed heterozygosity 0.55 and 0.53, expected heterozygosity 0.56 and 0.52, unbiased expected heterozygosity 0.57 and 0.52, for reintroduced and remnant populations, respectively. Sea otter population structure was greatest between the Northern and Southern sea otters with further structuring in Northern sea otters into Western, Central, and Southeast populations (including the reintroduced populations). Migrant analyses suggest the successful reintroductions and growth of remnant groups have enhanced connectivity and gene flow between populations throughout many of the sampled Northern populations. We recommend that future management actions for the Southern sea otter focus on future reintroductions to fill the gap between the California and Washington populations ultimately restoring gene flow to the isolated California population.     

Dispersal via stream corridors structures populations of the endangered St. Francis’ satyr butterfly (Neonympha mitchellii francisci)

Habitat fragmentation may reduce gene flow and population viability of rare species. We tested whether riparian corridors enhanced gene flow and if human habitat modification between riparian corridors subsequently reduced dispersal and gene flow of a wetland butterfly, the US federally endangered St. Francis’ satyr butterfly (Neonympha mitchellii francisci). We surveyed nine populations throughout the taxon’s range using five polymorphic microsatellite loci. We found that genetic diversity of N. m. francisci was relatively high despite its restricted distribution, and that there is little evidence of population bottlenecks or extensive inbreeding within populations. We found substantial gene flow and detectable first generation migration, suggesting that N. m. francisci is unlikely to be currently endangered by genetic factors. Pairwise population differentiation and clustering indicate some structuring between populations on different drainages and suggest that dispersal probably occurs mainly via a stepping stone from the closest riparian corridors. However, genetic differentiation between geographically close populations suggests that isolation by distance is not solely responsible for population structure, and that management actions should be targeted at maintaining connectivity of riparian and upland habitats.     

Population structure,connectivity, and demographic history of an apex marine predator,the bull shark Carcharhinus leucas

Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large‐bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC‐RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.     

The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym)

A primary goal of molecular ecology is to understand the influence of abiotic factors on the spatial distribution of genetic variation. Features including altitudinal clines, topography and landscape characteristics affect the proportion of suitable habitat, influence dispersal patterns, and ultimately structure genetic differentiation among populations. We studied the effects of altitude and topography on genetic variation of long-toed salamanders (Ambystoma macrodactylum), a geographically widespread amphibian species throughout northwestern North America. We focused on 10 low altitude sites (< 1200 m) and 11 high-altitude sites in northwestern Montana and determined multilocus genotypes for 549 individuals using seven microsatellite loci. We tested four hypotheses: (1) gene flow is limited between high- and low-altitude sites; and, (2) gene flow is limited among high-altitude sites due to harsh habitat and extreme topographical relief between sites; (3) low-altitude sites exhibit higher among-site gene flow due to frequent flooding events and low altitudinal relief; and (4) there is a negative correlation between altitude and genetic variation. Overall F(ST) values were moderate (0.08611; P < 0.001). Pairwise F(ST) estimates between high and low populations and a population graphing method supported the hypothesis that low-altitude and high-altitude sites, taken together, are genetically differentiated from each other. Also as predicted, gene flow is more prominent among low-altitude sites than high-altitude sites; low-altitude sites had a significantly lower F(ST) (0.03995; P < 0.001) than high altitude sites (F(ST) = 0.10271; P < 0.001). Use of Bayesian analysis of population structure (BAPS) resulted in delineation of 10 genetic groups, two among low-altitude populations and eight among high-altitude populations. In addition, within high altitude populations, basin-level genetic structuring was apparent. A nonequilibrium algorithm for detecting current migration rates supported these population distinctions. Finally, we also found a significant negative correlation between genetic diversity and altitude. These results are consistent with the hypothesis that topography and altitudinal gradients shape the spatial distribution of genetic variation in a species with a broad geographical range and diverse life history. Our study sheds light on which key factors limit dispersal and ultimately species' distributions.     

Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana

Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.     

Using occupancy models to investigate space partitioning between two sympatric large predators, the jaguar and puma in central Brazil

Coexistence of sympatric species is mediated by resource partitioning. Pumas occur sympatrically with jaguars throughout most of the jaguar's range but few studies have investigated space partitioning between both species. Here, camera trapping and occupancy models accounting for imperfect detection were employed in a Bayesian framework to investigate space partitioning between the jaguar and puma in Emas National Park (ENP), central Brazil. Jaguars were estimated to occupy 54.1% and pumas 39.3% of the sample sites. Jaguar occupancy was negatively correlated with distance to water and positively correlated with the amount of dense habitat surrounding the camera trap. Puma occupancy only showed a weak negative correlation with distance to water and with jaguar presence. Both species were less often present at the same site than expected under independent distributions. Jaguars had a significantly higher detection probability at cameras on roads than at off-road locations. For pumas, detection was similar on and off-road. Results indicate that both differences in habitat use and active avoidance shape space partitioning between jaguars and pumas in ENP. Considering its size, the jaguar is likely the competitively dominant of the two species. Owing to its habitat preferences, suitable jaguar habitat outside the park is probably sparse. Consequently, the jaguar population is likely largely confined to the park, while the puma population is known to extend into ENP's surroundings.     

Models of Regional Habitat Quality and Connectivity for Pumas (Puma concolor) in the Southwestern United States

The impact of landscape changes on the quality and connectivity of habitats for multiple wildlife species is of global conservation concern. In the southwestern United States, pumas (Puma concolor) are a well distributed and wide-ranging large carnivore that are sensitive to loss of habitat and to the disruption of pathways that connect their populations. We used an expert-based approach to define and derive variables hypothesized to influence the quality, location, and permeability of habitat for pumas within an area encompassing the entire states of Arizona and New Mexico. Survey results indicated that the presence of woodland and forest cover types, rugged terrain, and canyon bottom and ridgeline topography were expected to be important predictors of both high quality habitat and heightened permeability. As road density, distance to water, or human population density increased, the quality and permeability of habitats were predicted to decline. Using these results, we identified 67 high quality patches across the study area, and applied concepts from electronic circuit theory to estimate regional patterns of connectivity among these patches. Maps of current flow among individual pairs of patches highlighted possible pinch points along two major interstate highways. Current flow summed across all pairs of patches highlighted areas important for keeping the entire network connected, regardless of patch size. Cumulative current flow was highest in Arizona north of the Colorado River and around Grand Canyon National Park, and in the Sky Islands region owing to the many small habitat patches present. Our outputs present a first approximation of habitat quality and connectivity for dispersing pumas in the southwestern United States. Map results can be used to help target finer-scaled analyses in support of planning efforts concerned with the maintenance of puma metapopulation structure, as well as the protection of landscape features that facilitate the dispersal process.     

Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured-exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.