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  1. Abstract Accurate predictions of ecological restoration outcomes are needed across the increasingly large landscapes requiring treatment following disturbances. However, observational studies often fail to account for nonrandom treatment application, which can result in invalid inference. Examining a spatiotemporally extensive management treatment involving post-fire seeding of declining sagebrush shrubs across semiarid areas of the western USA over two decades, we quantify drivers and consequences of selection biases in restoration using remotely sensed data. From following more than 1,500 wildfires, we find treatments were disproportionately applied in more stressful, degraded ecological conditions. Failure to incorporate unmeasured drivers of treatment allocation led tomore »the conclusion that costly, widespread seedings were unsuccessful; however, after considering sources of bias, restoration positively affected sagebrush recovery. Treatment effects varied with climate, indicating prioritization criteria for interventions. Our findings revise the perspective that post-fire sagebrush seedings have been broadly unsuccessful and demonstrate how selection biases can pose substantive inferential hazards in observational studies of restoration efficacy and the development of restoration theory.« less
    Free, publicly-accessible full text available December 1, 2023
  2. Abstract Open science and open data within scholarly research programs are growing both in popularity and by requirement from grant funding agencies and journal publishers. A central component of open data management, especially on collaborative, multidisciplinary, and multi-institutional science projects, is documentation of complete and accurate metadata, workflow, and source code in addition to access to raw data and data products to uphold FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although best practice in data/metadata management is to use established internationally accepted metadata schemata, many of these standards are discipline-specific making it difficult to catalog multidisciplinary data and data products inmore »a way that is easily findable and accessible. Consequently, scattered and incompatible metadata records create a barrier to scientific innovation, as researchers are burdened to find and link multidisciplinary datasets. One possible solution to increase data findability, accessibility, interoperability, reproducibility, and integrity within multi-institutional and interdisciplinary projects is a centralized and integrated data management platform. Overall, this type of interoperable framework supports reproducible open science and its dissemination to various stakeholders and the public in a FAIR manner by providing direct access to raw data and linking protocols, metadata and supporting workflow materials.« less
    Free, publicly-accessible full text available December 1, 2023
  3. Free, publicly-accessible full text available June 7, 2023
  4. The Albany pitcher plant, Cephalotus follicularis , has evolved cup-shaped leaves and a carnivorous habit completely independently from other lineages of pitcher plants. It is the only species in the family Cephalotaceae and is restricted to a small region of Western Australia. Here, we used metabarcoding to characterize the bacterial and eukaryotic communities living in C. follicularis pitchers at two different sites. Bacterial and eukaryotic communities were correlated in both richness and composition; however, the factors associated with richness were not the same across bacteria and eukaryotes, with bacterial richness differing with fluid color, and eukaryotic richness differing with themore »concentration of DNA extracted from the fluid, a measure roughly related to biomass. For turnover in composition, the variation in both bacterial and eukaryotic communities primarily differed with fluid acidity, fluid color, and sampling site. We compared C. follicularis -associated community diversity with that of Australian Nepenthes mirabilis , as well as a global comparison of Southeast Asian Nepenthes and North American Sarracenia . Our results showed similarity in richness with communities from other pitcher plants, and specific bacterial taxa shared among all three independent lineages of pitcher plants. Overall, we saw convergence in richness and particular clades colonizing pitcher plants around the world, suggesting that these highly specialized habitats select for certain numbers and types of inhabitants.« less
    Free, publicly-accessible full text available June 6, 2023
  5. Abstract Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly formore »an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2 Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly-repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.« less
    Free, publicly-accessible full text available May 14, 2023
  6. Free, publicly-accessible full text available May 1, 2023
  7. Gambino, Michela (Ed.)
    ABSTRACT The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure thatmore »suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range.« less
    Free, publicly-accessible full text available April 26, 2023
  8. Food availability is a primary factor limiting the abundance of wild populations, but quantifying it requires an understanding of when and where prey are vulnerable to predators. Salmonid fishes in streams are commonly thought to forage on drifting aquatic invertebrates during daylight hours. However, past studies also report benthic and nocturnal foraging despite the predominant view of salmonids as diurnal drift-feeding predators. We used instream videography to assess foraging mode and energy intake for stream-dwelling Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri. We recorded the foraging behavior of wild fish with a waterproof video camera and estimated energy intake based onmore »fish size, foraging rate, retention rate, and caloric values of prey. Fish captured prey primarily from the water column and surface, targeting drifting invertebrates during daytime hours; however, they also foraged from the stream benthos and during nighttime. Yellowstone Cutthroat Trout foraging rate was most strongly related to foraging location in the stream, diel period, and month. Energy intake was highest from daytime drift-foraging behavior and exceeded a modeled metabolic limit of food intake during October and November. Nocturnal and benthic foraging contributed the smallest proportion of total foraging attempts but was observed over all months of our study and sometimes comprised up to 30% of estimated energy intake. Our results indicate that Yellowstone Cutthroat Trout in streams acquire most of the food intake as daytime drift-feeding predators.« less
    Free, publicly-accessible full text available March 21, 2023
  9. Free, publicly-accessible full text available January 1, 2023
  10. Free, publicly-accessible full text available December 1, 2022