Quantifying functional connectivity: The role of breeding habitat, abundance, and landscape features on range-wide gene flow in sage-grouse.

Functional connectivity, quantified using landscape genetics, can inform conservation through the identification of factors linking genetic structure to landscape mechanisms. We used breeding habitat metrics, landscape attributes, and indices of grouse abundance, to compare fit between structural connectivity and genetic differentiation within five long-established Sage-Grouse Management Zones (MZ) I-V using microsatellite genotypes from 6,844 greater sage-grouse (Centrocercus urophasianus) collected across their 10.7 million-km2 range. We estimated structural connectivity using a circuit theory-based approach where we built resistance surfaces using thresholds dividing the landscape into "habitat" and "nonhabitat" and nodes were clusters of sage-grouse leks (where feather samples were collected using noninvasive techniques). As hypothesized, MZ-specific habitat metrics were the best predictors of differentiation. To our surprise, inclusion of grouse abundance-corrected indices did not greatly improve model fit in most MZs. Functional connectivity of breeding habitat was reduced when probability of lek occurrence dropped below 0.25 (MZs I, IV) and 0.5 (II), thresholds lower than those previously identified as required for the formation of breeding leks, which suggests that individuals are willing to travel through undesirable habitat. The individual MZ landscape results suggested terrain roughness and steepness shaped functional connectivity across all MZs. Across respective MZs, sagebrush availability (<10%-30%; II, IV, V), tree canopy cover (>10%; I, II, IV), and cultivation (>25%; I, II, IV, V) each reduced movement beyond their respective thresholds. Model validations confirmed variation in predictive ability across MZs with top resistance surfaces better predicting gene flow than geographic distance alone, especially in cases of low and high differentiation among lek groups. The resultant resistance maps we produced spatially depict the strength and redundancy of range-wide gene flow and can help direct conservation actions to maintain and restore functional connectivity for sage-grouse.

Developing approaches for linear mixed modeling in landscape genetics through landscape-directed dispersal simulations.

Dispersal can impact population dynamics and geographic variation, and thus, genetic approaches that can establish which landscape factors influence population connectivity have ecological and evolutionary importance. Mixed models that account for the error structure of pairwise datasets are increasingly used to compare models relating genetic differentiation to pairwise measures of landscape resistance. A model selection framework based on information criteria metrics or explained variance may help disentangle the ecological and landscape factors influencing genetic structure, yet there are currently no consensus for the best protocols. Here, we develop landscape-directed simulations and test a series of replicates that emulate independent empirical datasets of two species with different life history characteristics (greater sage-grouse; eastern foxsnake). We determined that in our simulated scenarios, AIC and BIC were the best model selection indices and that marginal R2 values were biased toward more complex models. The model coefficients for landscape variables generally reflected the underlying dispersal model with confidence intervals that did not overlap with zero across the entire model set. When we controlled for geographic distance, variables not in the underlying dispersal models (i.e., nontrue) typically overlapped zero. Our study helps establish methods for using linear mixed models to identify the features underlying patterns of dispersal across a variety of landscapes.

Diffuse migratory connectivity in two species of shrubland birds: evidence from stable isotopes.

Connecting seasonal ranges of migratory birds is important for understanding the annual template of stressors that influence their populations. Brewer's sparrows (Spizella breweri) and sagebrush sparrows (Artemisiospiza nevadensis) share similar sagebrush (Artemisia spp.) habitats for breeding but have different population trends that might be related to winter location. To link breeding and winter ranges, we created isoscapes of deuterium [stable isotope ratio (δ) of deuterium; δ2H] and nitrogen (δ15N) for each species modeled from isotope ratios measured in feathers of 264 Brewer's and 82 sagebrush sparrows and environmental characteristics at capture locations across their breeding range. We then used feather 2Hf and 15Nf measured in 1,029 Brewer's and 527 sagebrush sparrows captured on winter locations in southwestern United States to assign probable breeding ranges. Intraspecies population mixing from across the breeding range was strong for both Brewer's and sagebrush sparrows on winter ranges. Brewer's sparrows but not sagebrush sparrows were linked to more northerly breeding locations in the eastern part of their winter range. Winter location was not related to breeding population trends estimated from US Geological Survey Breeding Bird Survey routes for either Brewer's or sagebrush sparrows. Primary drivers of population dynamics are likely independent for each species; Brewer's and sagebrush sparrows captured at the same winter location did not share predicted breeding locations or population trends. The diffuse migratory connectivity displayed by Brewer's and sagebrush sparrows measured at the coarse spatial resolution in our analysis also suggests that local environments rather than broad regional characteristics are primary drivers of annual population trends.

Modeling ecological minimum requirements for distribution of greater sage-grouse leks: implications for population connectivity across their western range, U.S.A.

Greater sage-grouse Centrocercus urophasianus (Bonaparte) currently occupy approximately half of their historical distribution across western North America. Sage-grouse are a candidate for endangered species listing due to habitat and population fragmentation coupled with inadequate regulation to control development in critical areas. Conservation planning would benefit from accurate maps delineating required habitats and movement corridors. However, developing a species distribution model that incorporates the diversity of habitats used by sage-grouse across their widespread distribution has statistical and logistical challenges. We first identified the ecological minimums limiting sage-grouse, mapped similarity to the multivariate set of minimums, and delineated connectivity across a 920,000 km(2) region. We partitioned a Mahalanobis D (2) model of habitat use into k separate additive components each representing independent combinations of species-habitat relationships to identify the ecological minimums required by sage-grouse. We constructed the model from abiotic, land cover, and anthropogenic variables measured at leks (breeding) and surrounding areas within 5 km. We evaluated model partitions using a random subset of leks and historic locations and selected D (2) (k = 10) for mapping a habitat similarity index (HSI). Finally, we delineated connectivity by converting the mapped HSI to a resistance surface. Sage-grouse required sagebrush-dominated landscapes containing minimal levels of human land use. Sage-grouse used relatively arid regions characterized by shallow slopes, even terrain, and low amounts of forest, grassland, and agriculture in the surrounding landscape. Most populations were interconnected although several outlying populations were isolated because of distance or lack of habitat corridors for exchange. Land management agencies currently are revising land-use plans and designating critical habitat to conserve sage-grouse and avoid endangered species listing. Our results identifying attributes important for delineating habitats or modeling connectivity will facilitate conservation and management of landscapes important for supporting current and future sage-grouse populations.

The human footprint in the west: a large-scale analysis of anthropogenic impacts.

Anthropogenic features such as urbanization, roads, and power lines, are increasing in western United States landscapes in response to rapidly growing human populations. However, their spatial effects have not been evaluated. Our goal was to model the human footprint across the western United States. We first delineated the actual area occupied by anthropogenic features, the physical effect area. Next, we developed the human footprint model based on the ecological effect area, the zone influenced by features beyond their physical presence, by combining seven input models: three models quantified top-down anthropogenic influences of synanthropic predators (avian predators, domestic dog and cat presence risk), and four models quantified bottom-up anthropogenic influences on habitat (invasion of exotic plants, human-caused fires, energy extraction, and anthropogenic wildland fragmentation). Using independent bird population data, we found bird abundance of four synanthropic species to correlate positively with human footprint intensity and negatively for three of the six species influenced by habitat fragmentation. We then evaluated the extent of the human footprint in relation to terrestrial (ecoregions) and aquatic systems (major rivers and lakes), regional management and conservation status, physical environment, and temporal changes in human actions. The physical effect area of anthropogenic features covered 13% of the western United States with agricultural land (9.8%) being most dominant. High-intensity human footprint areas (class 8-10) overlapped highly productive low-elevation private landholdings and covered 7% of the western United States compared to 48% for low-intensity areas (class 1-3), which were confined to low-productivity high-elevation federal landholdings. Areas within 1 km of rivers were more affected by the human footprint compared to lakes. Percentage human population growth was higher in low-intensity human footprint areas. The disproportional regional effects of the human footprint on landscapes in the western United States create a challenge to management of ecosystems and wildlife populations. Using footprint models, managers can plan land use actions, develop restoration scenarios, and identify areas of high conservation value at local landscapes within a regional context. Moreover, human footprint models serve as a tool to stratify landscapes for studies investigating floral and faunal response to human disturbance intensity gradients.

GIS-based niche modeling for mapping species' habitat.

Ecological "niche modeling" using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.

Landscape Characteristics of Fragmented Shrubsteppe Habitats and Breeding Passerine Birds.

We examined the influence of local and landscape-level attributes of fragmented habitats in shrubsteppe habitats on the breeding distributions of Sage (Amphispiza belli) and Brewer's (Spizella breweri) Sparrows, Sage Thrashers (Oreoscoptes montanus), Horned Larks (Eremophila alpestris), and Western Meadowlarks (Sturnella neglecta) in the Snake River Plains of southwestern Idaho. We developed habitat (resource) selection models for each species by combining bird counts conducted from 1991 through 1933 with local vegetation characteristics and landscape attributes derived from satellite imagery. Site selection by shrubsteppe species (Sage and Brewer's Sparrows, and Sage Thrashers) depended on local vegetation cover and landscape features, such as the patch size of shrub habitats or the spatial similarity of sites. Marginal sites for these species (with species present in one of three years) were intermediate between unoccupied (never present) and occupied sites along environmental gradients characterized by increasing size of shrub habitat patches and total shrub cover and by decreasing disturbance. Horned Larks and Western Meadowlarks, typical grassland species, were not sensitive to landscape features, and their occupancy depended on the amount of grassland or shrub cover. In contrast to shrubsteppe species, sites that varied by occupancy rates of Western Meadowlarks did not significantly differ in vegetation or landscape components. Our results demonstrate that fragmentation of shrubsteppe significantly influenced the presence of shrub-obligate species. Because of restoration difficulties, the disturbance of semiarid shrubsteppe may cause irreversible loss of habitat and significant long-term consequences for the conservation of shrub-obligate birds. Características del paisaje en ambientes fragmentados de estepas arbustivas y pájaros paserínidos en estado reproductivo.

Resumen: Examinamos la influencia de los atributos a nivel local y del paisaje de los hábitats fragmentados dentro de ambientes de estepas arbustivas, sobre las distribucion reproductiva de los paserinidos Amphispiza belli y Spizella breweri, Oreoscoptes montanus, Eremophila alpestris y Sturnella neglecta en las planicies del Río Snake del Sudoeste de Idaho. Desarrollamos modelos de selección de hábitats (recursos) para cada especie, combinando conteos de pájaros llevados a cabo entre 1991 y 1993 con características de la vegetación local y los atributos del hábitat derivados de imágenes de satelite. La selección de los sitios por parte de las especies de arbustos de las escarpas o pendientes (Amphispiza belli y Spizella breweri) dependió de la cobertura de la vegetación local y las características del paisaje, tales como el tamaño de los parches de los ambientes arbustivos o similitud espacial de los sitios. Los sitios marginales para esas especies (aquellos con las especies presentes en solo 1 de los 3 años) fueron intermedios entre los desocupados (nunca presentes) y los sitios ocupados, a lo largo de gradientes ambientales caracterizados por un incremento en el tamaño de los parches del ambiente arbustivo y la cobertura total de arbustos y un decrecimiento en la perturbación. Eremophila alpestris y Sturnella neglecta, especies típicas de pastizales, no fueron sensibles a las características del paisaje y dependieron de la cantidad de cobertura de pastizal o de arbustos. En forma opuesta a las especies de las estepas arbustivas, los sitos que variaron en cuanto al grado de ocupación de Sturnella neglecta, no presentaron variaciones significativas en los components de la vegetación o del paisaje. Nuestros resultados demuestran que la fragmentacion del paisaje de estepas arbustivas influenció significativamente la presencia de especies asociadas a los arbustos. Debido a las dificultades en la restauración, la perturbación de ambientes semi-áridos de estepas arbustivas puede causar la pérdida irreversible del hábitat y tener consecuencias significativas a largo plazo para la conservación de los pájaros asociados a los arbustos.