Mass mortality events (MMEs) are large-scale, rapid die-offs resulting in extreme inputs of carrion biomass. Recent work demonstrates the effects of increasing carrion biomass on plant communities modulated by vertebrate scavengers and herbivores. However, the mechanisms underlying plant response to MMEs remain unclear. We hypothesized that carrion decomposition would interact with vertebrate herbivory and scavenging to generate distinct ecological filters on plants grouped by three seed dormancy classes (no dormancy, physiological dormancy, and physical dormancy). We designed a replicated field experiment crossing two levels of carrion biomass (~30 kg and ~360 kg) with three levels of vertebrate exclusion (open/no exclusion, scavenger exclusion, and herbivore exclusion) to quantify plant extirpation and colonization, plant performance, and the response of simulated seed bank and seed rain. We measured carrion decomposition rate, plant tissue nutrients (N, P, and K), seed survival, plant height, flower production, and plant community changes over 3 years. Carrion biomass levels associated with mass mortality increased plant tissue nutrients and plant extirpation and decreased seed bank survival, likely promoting plant colonization from seed rain. Vertebrate exclusion determined colonization probability in different ways, depending on seed dormancy classes. Vertebrate scavenger exclusion delayed decomposition, and the resulting environment favored the colonization of plants with impermeable seed coats (physical dormancy). In contrast, vertebrate herbivore exclusion promoted rapid germinators (no dormancy) that arrived as seed rain and quickly capitalized on the nutrient-rich exposed soil. With both functional roles intact (open/no exclusion), vertebrate scavenging ameliorated the negative effects of decomposition on seeds and plants, and selective herbivory on nutrient-rich plant tissue reduced overall plant height and flower production. The activity of both functional roles favored plants of the dominant physiological seed dormancy class and those with physical dormancy. Our results suggest that seed response to carrion decomposition and vertebrate functional activity can inform plant community response to MMEs.

1. Anthropogenic subsidies to native predators can have cascading effects on sensitive prey populations, but the spatial mechanisms behind these effects are often unknown. 2. We used a stable isotope mixing model to reconstruct spatially naïve assimilated diets of common raven (Corvus corax) chicks and then used regression analysis to investigate landscape patterns in assimilated chick diet, with particular respect to the eggs and chicks of greater sage-grouse (Centrocercus urophasianus). 3. Assimilated raven diets were primarily composed of mammal carrion, followed by anthropogenic food and sage-grouse eggs and chicks. 4. Raven diets showed landscape gradients, whereby raven chicks in nests near active greater sage-grouse breeding leks consumed a higher proportion of sage-grouse eggs, sage-grouse chicks, and insects in their diet and less mammal carrion. A majority of raven nests on anthropogenic nesting structures (78.7%) were within 5 km of the nearest sage-grouse lek. Ravens nesting in high-probability greater sage-grouse nesting habitat consumed more insects and plants and less mammal carrion. 5. In landscapes devoid of natural raven nesting substrates, such as our study area, anthropogenic nesting substrates can ‘anchor’ breeding ravens nearer to greater sage-grouse leks, with concomitant increases in raven predation on greater sage-grouse nests. Curtailment of anthropogenic nesting substrates within 5 km of a sage-grouse lek may have a disproportionately positive impact on sage-grouse populations. More generally, these findings highlight that the spatial arrangement of anthropogenic subsidies can result in indirect interactions between humans and predators with direct implications for predators and prey.

Data, statistical analysis script, and supplementary material for manuscript on the role of deep rooting in switchgrass stress tolerance in low nitrogen and water conditions. Marcus Griffiths, Xueyan Wang, Kundan Dhakal, Haichao Guo, Anand Seethepalli, Yun Kang, Larry M York. Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.), Journal of Experimental Botany, Volume 73, Issue 3, 27 January 2022, Pages 967–979, https://doi.org/10.1093/jxb/erab437 The ZIP file contains: SWG3_dataprocessing.R - Statistics script. Requires all CSV data files in the directory. User needs to set working directory to location of this script and the CSV data files before running. SWG3...csv - 5 CSV data files required by the R script. Supplementary.docx - Not required for statistics. Accompany supplementary tables and figures for the manuscript.

Data, statistical analysis script, and supplementary material for manuscript on the role of deep rooting in switchgrass stress tolerance in low nitrogen and water conditions. Marcus Griffiths, Xueyan Wang, Kundan Dhakal, Haichao Guo, Anand Seethepalli, Yun Kang, Larry M York. Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.), Journal of Experimental Botany, Volume 73, Issue 3, 27 January 2022, Pages 967–979, https://doi.org/10.1093/jxb/erab437 The ZIP file contains: SWG3_dataprocessing.R - Statistics script. Requires all CSV data files in the directory. User needs to set working directory to location of this script and the CSV data files before running. SWG3...csv - 5 CSV data files required by the R script. Supplementary.docx - Not required for statistics. Accompany supplementary tables and figures for the manuscript.

This repository contains tabular data, R statistical code, protocols, and hardware plans associated with the following manuscript: A multiple ion-uptake phenotyping platform reveals shared mechanisms that affect nutrient uptake by maize roots Marcus Griffiths, Sonali Roy, Haichao Guo, Anand Seethepalli, David Huhman, Yaxin Ge, Robert E. Sharp, Felix B. Fritschi, Larry M. York Plant Physiology; doi: https://doi.org/10.1093/plphys/kiaa080 Equipment designs.zip - Contains the hardware plans, parts lists, and experimental protocol ImageJ_macro.zip - Contains scripts to use within ImageJ to segment images to calculate leaf area Supplementary_Data.zip - Contains the actual supplemental figures and tables for the manuscript as well as RNAseq data R code & raw data.zip - Contains a single .R text file containing all the R code to generate all the figures and and supplemental figures from the include raw data files E-mail mgriffiths at danforthcenter.org or lmyork at noble.org with any questions. Version 1 was used for the preprint. Version 2 was used for the final submitted manuscript. Version 3 is the final published version.

This repository contains tabular data, R statistical code, protocols, and hardware plans associated with the following manuscript: A multiple ion-uptake phenotyping platform reveals shared mechanisms that affect nutrient uptake by maize roots Marcus Griffiths, Sonali Roy, Haichao Guo, Anand Seethepalli, David Huhman, Yaxin Ge, Robert E. Sharp, Felix B. Fritschi, Larry M. York Plant Physiology; doi: https://doi.org/10.1093/plphys/kiaa080 Equipment designs.zip - Contains the hardware plans, parts lists, and experimental protocol ImageJ_macro.zip - Contains scripts to use within ImageJ to segment images to calculate leaf area Supplementary_Data.zip - Contains the actual supplemental figures and tables for the manuscript as well as RNAseq data R code & raw data.zip - Contains a single .R text file containing all the R code to generate all the figures and and supplemental figures from the include raw data files E-mail mgriffiths at danforthcenter.org or lmyork at noble.org with any questions. Version 1 was used for the preprint. Version 2 was used for the final submitted manuscript. Version 3 is the final published version.

This repository contains a PDF written protocol with figures describing a method for measuring root respiration using an infrared gas analyzer (LI-850) and the R script necessary for processing the text files to derive CO₂ flux. Just download the ZIP file, unzip locally, open either the PDF or the .R file. root_respiration_protocol.pdf - The illustrated protocol includes instruments and parts needed. root_respiration_script.R - A script for processing the included 15 .txt files as examples from a LI-850 Gas Analyzer and extract absolute CO₂ flux with example code for how to incorporate root mass or length to derive specific root respiration. It is intended to run directly in RStudio and will automatically set the working directory in that case. Please cite this repository if the protocol or R script is used in your work. Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2020). Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4247873 The first manuscript using and describing this method is available: Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2021). Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. New Phytologist. DOI: 10.1111/nph.17329

This repository contains a PDF written protocol with figures describing a method for measuring root respiration using an infrared gas analyzer (LI-850) and the R script necessary for processing the text files to derive CO₂ flux. Just download the ZIP file, unzip locally, open either the PDF or the .R file. root_respiration_protocol.pdf - The illustrated protocol includes instruments and parts needed. root_respiration_script.R - A script for processing the included 15 .txt files as examples from a LI-850 Gas Analyzer and extract absolute CO₂ flux with example code for how to incorporate root mass or length to derive specific root respiration. It is intended to run directly in RStudio and will automatically set the working directory in that case. Please cite this repository if the protocol or R script is used in your work. Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2020). Protocol and data analysis scripts for high-throughput phenotyping of specific root respiration [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4247873 The first manuscript using and describing this method is available: Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., York, L. M. (2021). Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. New Phytologist. DOI: 10.1111/nph.17329

This repository contains the root data, GEMMA files, and R code for generating the statistics and figures used in a preprint describing high-throughput phenotyping of root respiration in winter wheat. Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture Haichao Guo, Habtamu Ayalew, Anand Seethepalli, Kundan Dhakal, Marcus Griffiths, Xue-Feng Ma, Larry M. York bioRxiv 2020.11.12.380238; doi: https://doi.org/10.1101/2020.11.12.380238 analysis.R - A script for processing the included 4 CSV files of collected data. It is intended to run directly in RStudio and will automatically set the working directory in that case. The GEMMA folder includes files as output from GEMMA for genetic analysis, as described in the methods section of the preprint. These files are required by the R code for making Manhattan plots and other output. It will automatically create an output folder and the output text and figure files. The protocol for the respiration measurements are available in a separate Zenodo repository: https://doi.org/10.5281/zenodo.4247873 Please cite this repository and the preprint if any data or R code is used in your work.

This repository contains the root data, GEMMA files, and R code for generating the statistics and figures used in a preprint describing high-throughput phenotyping of root respiration in winter wheat. Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture Haichao Guo, Habtamu Ayalew, Anand Seethepalli, Kundan Dhakal, Marcus Griffiths, Xue-Feng Ma, Larry M. York bioRxiv 2020.11.12.380238; doi: https://doi.org/10.1101/2020.11.12.380238 analysis.R - A script for processing the included 4 CSV files of collected data. It is intended to run directly in RStudio and will automatically set the working directory in that case. The GEMMA folder includes files as output from GEMMA for genetic analysis, as described in the methods section of the preprint. These files are required by the R code for making Manhattan plots and other output. It will automatically create an output folder and the output text and figure files. The protocol for the respiration measurements are available in a separate Zenodo repository: https://doi.org/10.5281/zenodo.4247873 Please cite this repository and the preprint if any data or R code is used in your work.