Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem.

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field-based estimates of fitness components and approximate Bayesian computation (ABC) procedures to estimate habitat-specific dispersal rates and characterize habitat quality in two-toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field-based observations indicated that birth and survival rates were similar in a sparsely shaded cacao farm and adjacent cattle pasture-forest mosaic. Sloth density was threefold higher in pasture compared with cacao, whereas home range size and overlap were greater in cacao compared with pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 single nucleotide polymorphism and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstorey can, in some cases, constitute lower-quality habitat than pasture-forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field-based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.

Effects of forest management on California Spotted Owls: implications for reducing wildfire risk in fire­prone forests.

Management of many North American forests is challenged by the need to balance the potentially competing objectives of reducing risks posed by high-severity wildfires and protecting threatened species. In the Sierra Nevada, California, concern about high-severity fires has increased in recent decades but uncertainty exists over the effects of fuel-reduction treatments on species associated with older forests, such as the California Spotted Owl (Strix occidentalis occidentalis). Here, we assessed the effects of forest conditions, fuel reductions, and wildfire on a declining population of Spotted Owls in the central Sierra Nevada using 20 years of demographic data collected at 74 Spotted Owl territories. Adult survival and territory colonization probabilities were relatively high, while territory extinction probability was relatively low, especially in territories that had relatively large amounts of high canopy cover (≥70%) forest. Reproduction was negatively associated with the area of medium-intensity timber harvests characteristic of proposed fuel treatments. Our results also suggested that the amount of edge between older forests and shrub/sapling vegetation and increased habitat heterogeneity may positively influence demographic rates of Spotted Owls. Finally, high-severity fire negatively influenced the probability of territory colonization. Despite correlations between owl demographic rates and several habitat variables, life stage simulation (sensitivity) analyses indicated that the amount of forest with high canopy cover was the primary driver of population growth and equilibrium occupancy at the scale of individual territories. Greater than 90% of medium-intensity harvests converted high-canopy-cover forests into lower-canopy-cover vegetation classes, suggesting that landscape-scale fuel treatments in such stands could have short-term negative impacts on populations of California Spotted Owls. Moreover, high-canopy-cover forests declined by an average of 7.4% across territories during our study, suggesting that habitat loss could have contributed to declines in abundance and territory occupancy. We recommend that managers consider the existing amount and spatial distribution of high-canopy forest before implementing fuel treatments within an owl territory, and that treatments be accompanied by a rigorous monitoring program.

Relation between occupancy and abundance for a territorial species, the California spotted owl.

Land and resource managers often use detection-nondetection surveys to monitor the populations of species that may be affected by factors such as habitat alteration, climate change, and biological invasions. Relative to mark-recapture studies, using detection-nondetection surveys is more cost-effective, and recent advances in statistical analyses allow the incorporation of detection probability, covariates, and multiple seasons. We examined the efficacy of using detection-nondetection data (relative to mark-recapture data) for monitoring population trends of a territorial species, the California Spotted Owl (Strix occidentalis occidentalis). We estimated and compared the finite annual rates of population change (λt ) and the resulting realized population change (Δt ) from both occupancy and mark-recapture data collected over 18 years (1993-2010). We used multiseason, robust-design occupancy models to estimate that territory occupancy declined during our study (Δt = 0.702, 95% CI 0.552-0.852) due to increasing territory extinction rates (ε(1993) = 0.019 [SE 0.012]; ε(2009) = 0.134 [SE 0.043]) and decreasing colonization rates (γ(1993) = 0.323 [SE 0.124]; γ(2009) = 0.242 [SE 0.058]). We used Pradel's temporal-symmetry model for mark-recapture data to estimate that the population trajectory closely matched the trends in territory occupancy (Δt = 0.725, 95% CI 0.445-1.004). Individual survival was constant during our study (φ(1993) = 0.816 [SE 0.020]; φ(2009) = 0.815 [SE 0.019]), whereas recruitment declined slightly (f(1993) = 0.195 [SE 0.032]; f(2009) = 0.160 [SE 0.023]). Thus, we concluded that detection-nondetection data can provide reliable inferences on population trends, especially when funds preclude more intensive mark-recapture studies.