Genome-wide association study of germline variants and breast cancer-specific mortality

BACKGROUND: We examined the associations between germline variants and breast cancer mortality using a large meta-analysis of women of European ancestry. METHODS: Meta-analyses included summary estimates based on Cox models of twelve datasets using ~10

Influence of local and landscape factors on distributional dynamics: a species-centred, fitness-based approach

In spatially structured populations, distributional dynamics are driven by the quantity, connectivity and quality of habitat. Because these drivers are rarely measured directly and simultaneously at relevant scales, information on their relative importance remains unclear. I assessed the influence of both direct and indirect measures of local habitat quality, and of landscape habitat amount and connectivity on long-term territory occupancy dynamics of non-migratory pygmy owls. Direct measures of local habitat quality based on territory-specific reproductive output had greater effects on distribution than landscape factors, but only when spatio-temporal fluxes in performance linked to environmental stochasticity and intraspecific competition were considered. When habitat quality was measured indirectly based on habitat structure, however, landscape factors had greater effects. Although all landscape factors were important, measures of landscape connectivity that were uncorrelated with habitat amount and based on attributes of matrix structure and habitat configuration that influence dispersal movements had greater effects than habitat effective area (amount weighted by quality). Moreover, the influence of connectivity (but not habitat effective area) depended on local habitat quality. Such results suggest the relative importance of local habitat quality in driving distribution has been underestimated and that conservation strategies should vary spatially depending on both local and landscape contexts.National Park Service; Tucson Audubon Society; TE Inc.; Defenders of Wildlife; Center for Biological Diversity; US Fish and Wildlife Service; Sonoran Joint Venture; Arizona Zoological Society; Sierra Club12 month embargo; Published online: 5 July 2017.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Figure S1; Appendix S1 from Influence of local and landscape factors on distributional dynamics: a species-centred, fitness-based approach

Distribution of territory patches and landscapes across the 20,000-km2 study area in northwest Mexico.; Models, factors, and methods used to describe variation in local habitat quality

Impacts of Riparian Restoration on Vegetation and Avifauna on Private and Communal Lands in Northwest Mexico and Implications for Future Efforts

Restoring and enhancing riparian vegetation on private and communal lands in Mexico is important for biodiversity conservation given the ecological significance of these areas and the scarcity of public protected areas. To enhance riparian vegetation and wildlife habitats and train local people in restoration techniques, we implemented restoration and outreach efforts on private and communal lands in the Sky Islands region of northwest Mexico. We fenced 475 ha of riparian zones from livestock, erected erosion-control structures, planted trees, and developed management agreements for cool-season grazing with landowners on 10 ranches across 3 sites in 2012-2013, then repaired fences and renegotiated agreements in 2017-2019. To foster evaluation, we used a before-after/control-impact design to measure attributes of vegetation structure and bird communities and compared baselines from 2012 with post-treatment estimates from 2019. As predicted, understory vegetation volume generally increased in treatments relative to controls (P = .09), especially when one treatment area with the lowest pre-treatment grazing impacts was censored (P = .01). Although canopy cover also increased, there was little differential change in treatments relative to controls (P > .23) due likely to longer time periods needed to realize responses. Densities of most focal bird populations varied across time periods in directions that typically matched observed changes in vegetation structure, but fewer species showed signs of differential positive change linked to treatments relative to controls. Densities of Yellow-breasted Chat, a key understory obligate and important focal species, increased in treatments relative to controls across sites, as did densities of Sinaloa Wren, which also use dense underbrush (P 8-fold) also suggesting positive impacts of treatments. Despite mixed results over a limited time period, these patterns suggest restoration efforts drove localized recovery of understory vegetation and associated bird populations, but benefits varied widely with environmental and social factors linked to management. Greater ecological benefits to riparian areas on private and communal lands in this region can be fostered by further incentivizing construction, maintenance, and proper use of restoration infrastructure, through education, and by building relationships based on trust and credibility with landowners.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Historical changes in bird communities at Quitobaquito Springs, Arizona and impacts of climate, spring flow, and shift from Indigenous to federal-agency management

For nearly a century, bird communities at the oasis of Quitobaquito Springs in the Sonoran Desert have attracted desert ecologists. This spring-fed oasis is among the most biologically and culturally significant sites in arid southwestern North America, but has experienced marked changes in management and is threatened by climate change, border, and other development. We assembled data on birds at Quitobaquito across 83 years (1939–2022) and evaluated the patterns and potential drivers of changes in communities. We found evidence of marked community shifts that included apparent loss and replacement of species dependent on riparian and wetland vegetation, mud flats, agricultural fields, and human settlements, to species that use deeper more open-water environments, generalists, and desertscrub. Strong associations between community composition and shift from Indigenous to federal-agency management, temperature, and spring flow suggest important drivers of change, but associations with precipitation and border development were weaker. Such patterns match those for bird communities at broader scales in nearby and other aridlands and indicate impacts of increasing aridification. Our work represents the first analysis of changes in faunal assemblages at Quitobaquito that quantitatively assesses potential drivers of change, and provides insights for management and conservation.24 month embargo; first published 12 October 2023This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Abundance and habitat relationships of breeding birds in the Sky Islands and adjacent Sierra Madre Occidental of northwest Mexico

The Sierra Madre Occidental and neighboring Madrean Sky Islands span a large and biologically diverse region of northwest Mexico and portions of the southwestern United States. Little is known about the abundance and habitat use of breeding birds in this region of Mexico, but such information is important for guiding conservation and management. We assessed densities and habitat relationships of breeding birds across Sky Island mountain ranges in Mexico and adjacent portions of the Sierra Madre from 2009 to 2012. We estimated densities at multiple spatial scales, assessed variation in densities among all major montane vegetation communities, and identified and estimated the effects of important habitat attributes on local densities. Regional density estimates of 65% of 72 focal species varied significantly among eight montane vegetation communities that ranged from oak savannah and woodland at low elevations to pine and mixed-conifer forest at high elevations. Greater proportions of species occurred at peak densities or were relatively restricted to mixed-conifer forest and montane riparian vegetation likely because of higher levels of structural or floristic diversity in those communities, but those species were typically rare or uncommon in the Sky Islands. Fewer species had peak densities in oak and pine-oak woodland, and species associated with those communities were often more abundant across the region. Habitat models often included the effects of broadleaf deciduous vegetation cover (30% of species), which, together with tree density and fire severity, had positive effects on densities and suggest ways for managers to augment and conserve populations. Such patterns combined with greater threats to high-elevation conifer forest and riparian areas underscore their value for conservation. Significant populations of many breeding bird species, including some that are of concern or were not known to occur regionally or in mountain ranges we surveyed, highlight the importance of conservation efforts in this area of Mexico.National Park Service; Desert Southwest Cooperative Ecosystem Studies Unit; U.S. Fish and Wildlife Service; Sky Island Alliance; Veolia Environment Foundation; University of Montana Graduate School12 month embargoThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Long-term changes in abundances of Sonoran Desert lizards reveal complex responses to climatic variation

Understanding how climatic variation affects animal populations and communities is essential for addressing threats posed by climate change, especially in systems where impacts are projected to be high. We evaluated abundance dynamics of five common species of diurnal lizards over 25 years in a Sonoran Desert transition zone where precipitation decreased and temperature increased across time, and assessed hypotheses for the influence of climatic flux on spatiotemporal variation in abundances. We repeatedly surveyed lizards in spring and summer of each year at up to 32 sites, and used hierarchical mixture models to estimate detection probabilities, abundances, and population growth rates. Among terrestrial species, abundances of a short-lived, winter-spring breeder increased markedly by an estimated 2375285% across time, while two larger spring-summer breeders with higher thermal preferences declined by up to 64%. Abundances of two arboreal species that occupy shaded and thus sheltered microhabitats fluctuated but did not decline systematically. Abundances of all species increased with precipitation at short lag times (151.5 yrs) likely due to enhanced food availability, but often declined after periods of high precipitation at longer lag times (254 yrs) likely due to predation and other biotic pressures. Although rising maximum daily temperatures (Tmax) are expected to drive global declines of lizards, associations with Tmax were variable and weak for most species. Instead, abundances of all species declined with rising daily minimum temperatures, suggesting degradation of cool refugia imposed widespread metabolic or other costs. Our results suggest climate warming and drying are having major impacts on lizard communities by driving declines of species with traits that augment exposure to abiotic extremes and by modifying species interactions. The complexity of patterns we report indicate that evaluating and responding to the influence of climate change on biodiversity must consider a broad array of ecological processes.U.S. National Park Service (NPS)12 month embargo; published online: 17 August 2017This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Factors influencing detectability and responses of Elf Owls to playback of conspecific vocalizations

Broadcasting conspecific vocalizations is commonly used to survey secretive, inconspicuous, and uncommon species of birds, but information about how response behaviors vary across temporal and broad spatial gradients is limited for most species despite the importance of such data for guiding survey efforts. We assessed response patterns and detection probability of Elf Owls (Micrathene whitneyi) across broad ecological gradients in the Sonoran and Chihuahuan deserts of Arizona that spanned much of their breeding range in the United States. From March to June 2015–2017, we examined response times and distances of an estimated 587 Elf Owls detected during playback surveys at 1488 stations along 121 transects (193 km). Additionally, from April to June 2010–2011 and 2016–2017, we examined detection probability during 255 playback experiments at occupied nests and modeled the influence of spatial, temporal, moon illumination, vegetation, conspecific densities, and weather-related factors on detection probability. During transect surveys, response times were rapid (mean = 2.0 min), with 75% of detections within 3 min. Owls often responded close to broadcast stations (mean = 103 m), with only 25% of responses at distances > 140 m and none > 400 m. Response times were faster and from greater distances in the more arid western portion of our study area. During playback experiments at nests, detection probability averaged 0.65 and declined with increasing time of night, time of season, and noise levels. Detection probability also declined with increasing distance from target owls, but at lower rates in the western than the eastern portion of our study area. Spatial variation in detectability was primarily due to surveyors failing to detect responding owls in areas with higher owl densities in more resource-rich environments in the east, not differences in underlying responsiveness. Our results suggest that 5 or 6 min surveys within ˜4 h of sunset and early in the breeding season will be most effective and that spacing survey stations from 100 to 150 m apart, depending on local densities and study objectives, is adequate for estimating occupancy and abundance with relatively low false absence rates.Bureau of Reclamation12 month embargo; first published: 06 August 2021This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Application of distance sampling for assessing abundance and habitat relationships of a rare Sonoran Desert cactus

Accurate abundance estimates of plant populations are fundamental to numerous ecological questions and for conservation. Estimating population parameters for rare or cryptic plant species, however, can be challenging and thus developing and testing new methods is useful. We assessed the efficacy of distance sampling for estimating abundance and habitat associations of the endangered Pima pineapple cactus (Coryphantha scheeri var. robustispina), a rare plant in the Sonoran Desert of southwestern North America that has traditionally been surveyed with census-based methods. Distance sampling (DS) involves measuring distances between focal objects and samples of lines or points, and modeling detection functions that adjust estimates for variation in detection probability (P). Although often used in animal systems, DS remains largely untested for plants. We encountered 105 live individuals along 36.9 km of transects in 11 study plots placed across much of the geographic range of the species, and estimated an average density of 1.47 individuals/ha (CV = 0.139). Compared to values from intensive censuses, density estimates from DS were underestimated by only 2.3% on average and highly correlated on the untransformed (r = 0.84) and logarithmic (r = 0.93) scales. Estimates of P averaged 0.49 and declined as soils became increasingly dominated by larger soil substrates, and somewhat with increasing vegetation volume and decreasing cactus height. Local densities increased with increasing slope and soil substrate size and decreased with increasing vegetation volume (P <= 0.024). Combined with careful survey design, DS offers an efficient method for estimating population parameters for uncommon and cryptic plants.12 month embargo; published online: 16 September 2019This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]