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Spatially-explicit individual-based simulation models provide a valuable tool for exploring complex ecological and evolutionary processes that are not easily empirically measured. Here, we present modifications of a spatially-explicit individual-based simulation model (CDMetaPOP) to accommodate a two-species system and simulations involving interspecific hybridization. We first describe how a hybrid (H) index is used to distinguish individuals of interspecific descent from those of either parental species. User-defined thresholds provide flexibility in the degree of admixture tolerated for classifying ‘pure’ individuals. We then detail relationships further informed by the H index, including individual growth, temperature-based fitness and selection, and mate preference behavior. Empirically derived species- and system-specific information can be incorporated into these relationships, for example, to produce differential growth among hybrids and parental species. Lastly, we demonstrate an application of this simulation framework by exploring the relative effects of temperature-based selection, mate preference behavior, and hybrid fitness on the rate and spatial extent of sympatric hybridization between two native riverine fish species, bull trout (Salvelinus confluentus) and Dolly Varden (Salvelinus malma), in the upper Skagit River system (United States and Canada). Results from this demonstration provide guidance for future empirical studies of bull trout, a federally threatened species. Understanding factors that contribute to the initiation and maintenance of hybridization, as well as the ecological and evolutionary consequences of this phenomenon, is of increasing importance given shifting species ranges due to large-scale landscape modification and a changing global climate. Our framework can be used to study a wide range of hybridization dynamics in any terrestrial or aquatic system, including comparisons of distinct environmental conditions or potential management responses.

Tropical ecosystem conversion to agriculture has caused widespread habitat loss and created fragmented landscapes composed of remnant forest patches embedded in a matrix of agricultural land uses. Non-traditional agricultural export (NTAE) crops such as pineapple are rapidly replacing multiuse landscapes characterized by a diverse matrix of pasture and smallholder crops with intensive, large-scale, monoculture plantations. Using an interdisciplinary approach, we conduct a case study to examine the coupled social and ecological implications of agricultural intensification in this region, with larger application to regions experiencing similar patterns of agricultural intensification. Guided by frameworks from both political and landscape ecology, we: (1) describe the social and economic implications of pineapple expansion, specifically the concentration of land, labor and financial resources, (2) quantify pineapple cultivation's spatial characteristics, and (3) assess the effects of pineapple expansion on surrounding forest ecosystems, on the agricultural matrix and on biodiversity conservation. Our results indicate that pineapple production concentrates land, labor, and financial resources, which has a homogenizing effect on the agricultural economy in the study region. This constrains farm-based livelihoods, with larger implications for food security and agricultural diversity. Landscape ecology analyses further reveal how pineapple production simplifies and homogenizes the agricultural matrix between forest patches, which is likely to have a negative effect on biodiversity. To offset the effects of pineapple expansion on social and environmental systems, we recommend developing landscape level land use planning capacity. Furthermore, agricultural and conservation policy reform is needed to promote landscape heterogeneity and economic diversity within the agricultural sector. Our interdisciplinary research provides a detailed examination of the social and ecological impacts of agricultural intensification in a tropical landscape, and offers recommendations for improvement relevant not only to our study region but to the many other tropical landscapes currently undergoing non-traditional agricultural export driven agricultural intensification.

Isolation of environmental DNA (eDNA) is becoming a valuable tool for detecting presence of rare or secretive aquatic species. The recent use of quantitative PCR (qPCR) with eDNA sampling presents the possibility of using this method to infer population abundance and status. This approach would be especially useful for species such as the Eastern hellbender (Cryptobranchus alleganiensis alleganiensis), a declining, secretive, aquatic salamander that requires intense field survey effort to study. In 2012, we conducted eDNA sampling at sites across the range of the species in North Carolina. Our objectives were to assess presence across 61 sites, test for a correlation of abundance and biomass with eDNA estimates at a subset of 23 sites, and sample at multiple spatial and temporal scales in three river systems. Overall, we detected hellbender eDNA at 33 sites, including all sites with 2012 hellbender records, 71% of all recent or historic sites with hellbender presence, and at nine sites that lack species occurrence records. We did not find a correlation between eDNA estimates and field survey counts of individuals or biomass. We detected a strong temporal increase in eDNA during the September breeding period, but no consistent evidence of a spatial relationship with eDNA. Overall, our results demonstrate the efficacy of eDNA for detecting hellbender populations. Furthermore, the potential utility of qPCR to assess population status in hellbenders requires further study and testing, although it may be promising for determining population reproductive status.

Individual behavior promotes genetic structure within many mammalian populations, yet few studies have explored coarse- and fine-scale structure associated with migration. Fewer still have considered the conservation implications of such structure in at-risk populations. Pronghorn ( Antilocapra americana ) inhabiting Yellowstone National Park are partially migratory, and strong adult fidelity to migratory strategy and breeding areas may promote social and genetic structure within this population. We used 18 nuclear DNA microsatellite loci and fecal samples from 47 individuals to quantify group divergence and pairwise relatedness of Yellowstone pronghorn. The genetics of this population are characterized by individual isolation by distance ( P = 0.009). Evidence for fine-scale social and genetic structure was strong, with mean relatedness between individuals declining rapidly with geographic distance (0–3 km) within areas selected by both migrants and non-migrants. On average, females sampled within social groups were related at the level of first cousins (mean R = 0.105 ± 0.192 SD). We found low differentiation of the population by migratory strategy ( F ST = 0.019), moderate differentiation among some summer use areas ( F ST ⩾ 0.033), and an excess of heterozygotes within all migrant groups ( F IS ⩽ −0.017). Weak and inconsistent substructure was detected using spatial and aspatial Bayesian clustering methods. Our results are the first to document fine-scale social and genetic structure in pronghorn, most likely organized along matrilines. Access to a majority of the total summer range available to this population is maintained by social inheritance and individual fidelity to areas of use. The maintenance and reestablishment of migratory routes may therefore hinge on the retention of experienced individuals, the strength of natal and adult philopatry, and the accessibility of seasonal habitat to pioneering females.

Among cooperatively breeding species, delayed dispersal provides an opportunity for older siblings to help rear young. There is considerable variation in the extent to which cooperative breeders delay dispersal, however, and while delayed dispersal may be a consequence of adaptive evolution favouring family living, evidence for a genetic basis is lacking. Furthermore, the extent to which dispersal behaviour itself is under direct selection, or evolves indirectly in response to selection on correlated life-history traits, remains unclear. We tested for evidence of inter- and intraspecific quantitative genetic variation in age at first dispersal in a reintroduced population of the red wolf, Canis rufus , that naturally hybridizes with the coyote, Canis latrans , which delays dispersal to a lesser extent than the red wolf. Using analyses based on individual relationships to population founders and sire–offspring regressions, we found evidence for intraspecific genetic variation in dispersal age in male, but not female, red wolves. We also found evidence for interspecific genetic variation, in that red wolves had later dispersal age than coyote–red wolf hybrids. Intraspecific variation in dispersal age was not explained by variation in social and environmental factors nor alternative targets of selection such as body mass or age at first reproduction. Thus, selection may act directly on dispersal-related behaviours. However, life-history traits may continue to be influential in creating interspecific differences in dispersal age, as hybrids also showed earlier reproduction. Our findings suggest that evolution of delayed dispersal may be due to both direct and indirect selection on existing quantitative genetic variation, and that genetic and environmental mechanisms underlying dispersal may differ between the sexes.

Land use change driven by exurban development can lead to dramatic alterations in the structure and function of landscapes. Residential development outside of urban and suburban zones can disrupt agricultural and forest management operations and ecosystem processes, increase community wildfire hazard, deplete groundwater resources, and lead to social conflict. We assessed two policy tools, urban growth boundaries and agricultural use zoning, for their potential to help manage growth and sustain the rural landscape. Using a survey-based model, we simulated the effects of the two policy tools on land use change and compared the results with predictions of land use change for two rural counties (4794 km 2 ) in northern Idaho developed in a previous project. We measured the effects of predicted exurban development using four measures: number of housing units predicted on productive agricultural lands, number of housing units predicted on a groundwater resource area, changes to a wildfire hazard index for residential structures, and the social acceptability of residential development patterns given current development preferences. The two policy tools impose in substantially different landscape-level residential development patterns when compared to the baseline change prediction and each other. Each tool resulted in a variety of tradeoffs between negative and positive effects among our measures of impact. Our findings demonstrate the importance of using multiple indicators to evaluate growth management and land protection policy tools for making land use planning decisions.

As rural landscapes experience increasing levels of residential development, the persistence of species that rely on them will depend on informed planning and management decisions. An understanding of habitat requirements is essential for setting priorities and developing landscape-level plans for the survival of these species. In many temperate rural landscapes, artificially created ponds may be the only wetlands available for aquatic reproduction by amphibians. The introduction of non-native fish into these ponds reduces survival and prohibits successful reproduction of many native pond-breeding amphibians. We surveyed 105 randomly selected wetlands in a primarily privately-owned, rural landscape in north Idaho, USA, for pond-breeding amphibian larvae in 2004 and 2005. We used an information theoretic multimodel inference and an algorithmic (random forests) approach to model habitat for each species based on local and landscape characteristics. We also used a mail survey to quantify how landowners value fish in their wetlands and their plans for future wetland development and fish stocking. Sixty-seven percent of pond owners reported that fishing in their pond was at least slightly important to them and 36% of owners indicated that they were at least 50% likely to add fish to their ponds in the next 5–10 years. Landscape change predictions for this area indicate that forests will become more open due to thinning; habitat models indicated that this is likely to be detrimental to long-toed salamanders and beneficial to Pacific treefrogs. Habitat models also indicate that Columbia spotted frog breeding sites consist of wetlands on flat ground with high solar insolation and that this species is sensitive to nearby development, indicating that as this landscape becomes further developed, this species may require habitat protection for persistence.

Little is known of the mating system of the swift fox or how it compares to other socially monogamous mammals. In a 4-year study of 188 swift foxes, we used microsatellite analysis at 11 loci along with spatial observations to investigate swift fox mating strategies. The mating strategies used by swift foxes were highly diverse. Previous field observations have indicated that the swift fox is socially monogamous. However, we found that extrapair mating was a common breeding strategy; 52% of offspring were sired by a male that was not the mate of their mother. There was also variation in the structure of social groups. Of 59 social groups, the most common consisted of a male and female pair (93% of social groups); however, four stable trios of both one female and two males (5%) and two females and one male (2%) were also evident. The trio groups were spatially associated, and at least one member of each trio was highly related to a member in at least one other trio. Swift foxes also engaged in mate switching, which refutes the prevailing hypothesis that they always mate for life. Thus, we found that the mating system of the swift fox is highly diverse and substantially more complex than previously believed. We discuss factors that may influence which strategies are adopted and whether they are adaptive.

We used non-invasive DNA hair-sampling and catch per unit effort (CPUE: grizzly bears detected per 1000 trap nights) to estimate relative density and population size for a threatened grizzly bear population in the North Cascade Ecosystem of Washington and British Columbia. We used linear, logistic, and linear through the origin regression analyses to estimate the relationship between catch per unit effort and grizzly bear density for seven other grizzly populations. One grizzly bear was detected during 5304 trap nights (CPUE=0.19) over 3 years in the North Cascades. This CPUE was much lower than in the other seven populations, including two threatened grizzly populations in the Cabinet-Yaak and Selkirk Mountain Ecosystems. The logistic model (curvilinear relationship) best fit the data (R2=0.927), and yielded density and population size estimates of 0.15 bears/100 km2 (90% CI=0.03–0.71) and six bears (90% CI=1–27), respectively. Natural recovery seems unlikely for the North Cascade grizzly bear population because the population has a high likelihood of extinction due to demographic and environmental stochastic effects associated with extremely small population numbers. We recommend population augmentation. DNA hair-sampling and catch per unit effort models can be a useful method to evaluate relative densities and numbers of animals in small, threatened grizzly bear populations when sample sizes are too small to yield traditional mark–recapture analysis.

The bear family (Ursidae) presents a number of phylogenetic ambiguities as the evolutionary relationships of the six youngest members (ursine bears) are largely unresolved. Recent mitochondrial DNA analyses have produced conflicting results with respect to the phylogeny of ursine bears. In an attempt to resolve these issues, we obtained 1916 nucleotides of mitochondrial DNA sequence data from six gene segments for all eight bear species and conducted maximum likelihood and maximum parsimony analyses on all fragments separately and combined. All six single-region gene trees gave different phylogenetic estimates; however, only for control region data was this significantly incongruent with the results from the combined data. The optimal phylogeny for the combined data set suggests that the giant panda is most basal followed by the spectacled bear. The sloth bear is the basal ursine bear, and there is weak support for a sister taxon relationship of the American and Asiatic black bears. The sun bear is sister taxon to the youngest clade containing brown bears and polar bears. Statistical analyses of alternate hypotheses revealed a lack of strong support for many of the relationships. We suggest that the difficulties surrounding the resolution of the evolutionary relationships of the Ursidae are linked to the existence of sequential rapid radiation events in bear evolution. Thus, unresolved branching orders during these time periods may represent an accurate representation of the evolutionary history of bear species.

Times Cited: 185; International audience; Noninvasive sampling allows genetic studies of free-ranging animals without the need to capture or even observe them, and thus allows questions to be addressed that cannot be answered using conventional methods. Initially, this sampling strategy promised to exploit fully the existing DNA-based technology for studies in ethology; conservation biology and population genetics. However, recent work now indicates the need for a more cautious approach, which includes quantifying the genotyping error rate. Despite this, many of the difficulties of noninvasive sampling will probably be overcome with improved methodology.