Linking Landscape-Scale Differences in Forage to Ungulate Nutritional Ecology

Understanding how habitat and nutritional condition affect ungulate populations is necessary for informing management, particularly in areas experiencing carnivore recovery and declining ungulate population trends.  Variations in forage species availability, plant phenological stage, and the abundance of forage make it challenging to understand landscape-level effects of nutrition on ungulates.  We developed an integrated spatial modeling approach to estimate landscape-level elk (Cervus elaphus) forage quality in two adjacent study areas that differed in coarse measures of habitat quality and related the consequences of differences in forage quality to elk body condition and pregnancy rates.  We found no support for differences in dry matter digestibility between plant samples or in phenological stage based on ground sampling plots in the two study areas.  Forage quality, measured as digestible forage biomass, varied among land cover types and between study areas. We found that altered plant composition following fires was the biggest driver of forage quality differences, suggesting that maintaining a mosaic of fire history and distribution will likely benefit ungulate populations.  Study area, lactation status and year affected fall body fat of adult female elk.  Elk in the study area exposed to lower quality summer range forage had lower nutritional condition entering winter.  These differences in nutritional condition resulted in differences in pregnancy rate, with average pregnancy rates of 89% for elk exposed to higher quality forage and 72% for elk exposed to lower quality forage.  Summer range forage quality has the potential to limit elk pregnancy rate and calf production, and these nutritional limitations may predispose elk to be more sensitive to the effects of harvest or predation.  Wildlife managers should identify ungulate populations that are nutritionally limited and recognize that these populations may be more impacted by recovering carnivores or harvest than populations inhabiting more productive summer habitats

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Cushion plant community data from an Andean alpine ecosystem in Venezuela

Site These data were collected in the northern-most reaches of the Andes Mountains in the Piedras Blancas páramo, Sierra de La Culata National Park, Venezuela, during January-March 2014 (dry season). Sites were located in the high Andean páramo (superpáramo), between 4250m-4350m, with slopes of 15-25 degrees, and on northeast facing aspects. We sampled three sites in a 5 km area: Rio Azul (8.8866, -70.8685), Avenida (8.8847, -70.8666), and Gloria (8.8928, -70.8714). Life in this region is subject to harsh and dynamic tropical alpine conditions.This region is the driest in Venezuela’s high alpine, with an annual precipitation of 860 mm (Pico El Águila weather station, 4,118 m). The soils at the study sites are coarse, shallow and subject to constant disturbance by needle-ice formation due to frequent freeze-thaw cycles in the soil. The plant community in our study sites sparsely covers the landscape (generally less than 50% cover) and the vegetation is highly clustered. This cover is partitioned into two strata, one dominated by giant rosettes and shrubs, and the other consisting of cushions, disperse grasses, forbs, cushions, and acaulescent rosettes. We studied the two most abundant cushion species in the area, Azorella julianii and Arenaria musciformis. A. julianii is commonly found in the northern Andes from Ecuador to Venezuela (3500-4700 m), while A. musciformis is present in Colombia and Venezuela (3500 and 4300 m). Soil Methods Measurements of soil relative water content (SWC) and organic matter (SOM) were performed by taking soil samples from 5 to 10 cm below the soil surface near midday on a clear day of the dry season (March 2014). One sample was taken from each of eight different haphazardly chosen cushions of Arenaria and Azorella and eight open sites away from the cushions influence (but always within 2-4 m from each replicate pair). SWC measurements were made by calculating the percentage of water in the sample through differences between wet and dry weights. SOM content determinations were obtained using the weight difference between a sample of dry soil, and the remnants of the sample after heating to 400 o C for 4 hours. For measuring shallow soil temperatures within each cushion species, we haphazardly chose three individuals with more than 30 cm in diameter and placed one replicate Onset HOBO TidbiT v2 sensor within each. Sensors were buried 2 cm below the leaf surface at the center of each cushion. Then, we haphazardly sampled three nearby open soil sites away from the direct influence of the cushions and placed one replicate temperature sensor in each, 2 cm below the soil surface. These nine sensors recorded temperatures every 15 minutes during five consecutive clear days between the 27 and 31st of March 2014. From each sensor´s data we calculated the mean, maximum and minimum temperatures and averaged them between the replicate sensors in each microhabitat (inside Azorella and Arenaria and in open areas). Vegetation Sampling Methods At each of the three study sites we haphazardly selected 35 individual cushions of each species within a 200 x 200 m area. For each individual, we placed a wire ring on the cushion and recorded the presence and number of individuals of all vascular plant species within. We defined individuals as ramets, as many species in the páramo are interconnected underground. Then, we randomly sampled open substrate 1 m from each cushion (in 35 paired samples for each cushion species) and measured richness and density within the wire rings in the same way we did in the cushion. In the case of Azorella, there were many cushions that exceeded a mean diameter of 50 cm. However, in the case of Arenaria, the majority of individuals in the population were smaller than that. Hence, we used a 40 cm diameter flexible sampling ring for Azorella (and the paired samples outside) and a 20 cm diameter ring for Arenaria (and paired samples). The area of the rings in each case was then used to calculate plant density for each species. We only sampled individual cushions with a minimum length in one dimension of at least 40 cm for Azorella and at least 20 cm for Arenaria

Reciprocal interactions between a facilitator, natives, and exotics in tropical alpine plant communities

Facilitation by nurse plants has received considerable attention, but the feedback effects of beneficiaries on the benefactor fitness remain comparatively unexplored. In particular, to our knowledge there have been no studies of feedback effects of exotic species on nurse plants. Furthermore, there have been few studies of how exotic plants interact with native beneficiaries, potentially generating indirect effects on the nurse. Here, through spatial association analyses, we estimate the reciprocal interactions between the cushion nurse-plant Arenaria musciformis, native beneficiaries, and the dominant exotic Rumex acetosella (a fast growing heliophile species) in a tropical alpine ecosystem of the Venezuelan Andes, locally known as páramos. We recorded the density of natives and the exotic within Arenaria cushions and in paired open areas at three sites and calculated Relative Interaction Indices (RII) to explore the effects of the cushion. Then, we analyzed the feedback effects of Rumex and the natives on the density of flowers produced by Arenaria. Finally, we analyzed how Rumex abundance is related to the abundance of native species inside and outside cushions. RIIs indicated a facilitative effect of cushions on the abundance of native plants, but no effect on Rumex. We found a negative relationship between the density of natives and cushion flower density, but no such relationship for Rumex. However, at high densities, Rumex was negatively correlated with the abundance of the natives both inside and outside of cushions. Our results suggest the possibility of complex reciprocal interactions between nurses, natives and exotics, and that native and exotic plants can differ in their feedback effects on nurse cushions. Native plants appeared to be facilitated by cushions and then develop a parasitic relationship with their nurses. In contrast, the exotic Rumex had a neutral interaction with the nurse, but competitive effects on the native beneficiary community, which could indirectly modulate the feedback effects of natives on the nurse. These results highlight the importance of analyzing direct and indirect reciprocal interactions and the impacts of exotic invaders for understanding alpine community assembly.Fil: Llambí, Luis D.. Universidad de Los Andes; VenezuelaFil: Hupp, Nicole. University of Montana; Estados UnidosFil: Sáez, Agustín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Callaway, Ragan. University of Montana; Estados Unido

Data from: Linking landscape-scale differences in forage to ungulate nutritional ecology

Understanding how habitat and nutritional condition affect ungulate populations is necessary for informing management, particularly in areas experiencing carnivore recovery and declining ungulate population trends. Variations in forage species availability, plant phenological stage, and the abundance of forage make it challenging to understand landscape-level effects of nutrition on ungulates. We developed an integrated spatial modeling approach to estimate landscape-level elk (Cervus elaphus) nutritional resources in two adjacent study areas that differed in coarse measures of habitat quality and related the consequences of differences in nutritional resources to elk body condition and pregnancy rates. We found no support for differences in dry matter digestibility between plant samples or in phenological stage based on ground sampling plots in the two study areas. Our index of nutritional resources, measured as digestible forage biomass, varied among landcover types and between study areas. We found that altered plant composition following fires was the biggest driver of differences in nutritional resources, suggesting that maintaining a mosaic of fire history and distribution will likely benefit ungulate populations. Study area, lactation status and year affected fall body fat of adult female elk. Elk in the study area exposed to lower summer range nutritional resources had lower nutritional condition entering winter. These differences in nutritional condition resulted in differences in pregnancy rate, with average pregnancy rates of 89% for elk exposed to higher nutritional resources and 72% for elk exposed to lower nutritional resources. Summer range nutritional resources have the potential to limit elk pregnancy rate and calf production, and these nutritional limitations may predispose elk to be more sensitive to the effects of harvest or predation. Wildlife managers should identify ungulate populations that are nutritionally limited and recognize that these populations may be more impacted by recovering carnivores or harvest than populations inhabiting more productive summer habitats

Data from: Linking landscape-scale differences in forage to ungulate nutritional ecology

Understanding how habitat and nutritional condition affect ungulate populations is necessary for informing management, particularly in areas experiencing carnivore recovery and declining ungulate population trends. Variations in forage species availability, plant phenological stage, and the abundance of forage make it challenging to understand landscape-level effects of nutrition on ungulates. We developed an integrated spatial modeling approach to estimate landscape-level elk (Cervus elaphus) nutritional resources in two adjacent study areas that differed in coarse measures of habitat quality and related the consequences of differences in nutritional resources to elk body condition and pregnancy rates. We found no support for differences in dry matter digestibility between plant samples or in phenological stage based on ground sampling plots in the two study areas. Our index of nutritional resources, measured as digestible forage biomass, varied among landcover types and between study areas. We found that altered plant composition following fires was the biggest driver of differences in nutritional resources, suggesting that maintaining a mosaic of fire history and distribution will likely benefit ungulate populations. Study area, lactation status and year affected fall body fat of adult female elk. Elk in the study area exposed to lower summer range nutritional resources had lower nutritional condition entering winter. These differences in nutritional condition resulted in differences in pregnancy rate, with average pregnancy rates of 89% for elk exposed to higher nutritional resources and 72% for elk exposed to lower nutritional resources. Summer range nutritional resources have the potential to limit elk pregnancy rate and calf production, and these nutritional limitations may predispose elk to be more sensitive to the effects of harvest or predation. Wildlife managers should identify ungulate populations that are nutritionally limited and recognize that these populations may be more impacted by recovering carnivores or harvest than populations inhabiting more productive summer habitats

elk_data

This file contains the fall elk body fat (IFBF) and pregnancy data used in analyses. For fall measurements, lactation status is included; in late-winter/spring measurements lactation status could not be determined. Age was estimated from tooth eruption and wear patterns. Pregnancy was estimated from PSPB levels in the blood. IFBF was estimated following the revised methods of Cook et al. (2010) that included an allometrically scaled MAXFAT index

Linking Phenological Indices from Digital Cameras in Idaho and Montana to MODIS NDVI

Digital cameras can provide a consistent view of vegetation phenology at fine spatial and temporal scales that are impractical to collect manually and are currently unobtainable by satellite and most aerial based sensors. This study links greenness indices derived from digital images in a network of rangeland and forested sites in Montana and Idaho to 16-day normalized difference vegetation index (NDVI) from NASA&rsquo;s Moderate Resolution Imaging Spectroradiometer (MODIS). Multiple digital cameras were placed along a transect at each site to increase the observational footprint and correlation with the coarser MODIS NDVI. Digital camera phenology indices were averaged across cameras on a site to derive phenological curves. The phenology curves, as well as green-up dates, and maximum growth dates, were highly correlated to the satellite derived MODIS composite NDVI 16-day data at homogeneous rangeland vegetation sites. Forested and mixed canopy sites had lower correlation and variable significance. This result suggests the use of MODIS NDVI in forested sites to evaluate understory phenology may not be suitable. This study demonstrates that data from digital camera networks with multiple cameras per site can be used to reliably estimate measures of vegetation phenology in rangelands and that those data are highly correlated to MODIS 16-day NDVI