Gompert, Zachariah

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DigitalCommons@USU

Utah State University DigitalCommons@USU Funded Research Records 3-20-2019 CAREER: An integrated approach to understanding selection and evolution in heterogeneous environments Zachariah Gompert Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/funded_research_data Recommended Citation Gompert, Z. (2019). CAREER: An integrated approach to understanding selection and evolution in heterogeneous environments. Utah State University. https://doi.org/10.26077/54T2-YG51 This Grant Record is brought to you for free and open access by DigitalCommons@USU. It has been accepted for inclusion in Funded Research Records by an authorized administrator of DigitalCommons@USU. For more information, please contact digitalcommons@usu.edu. 1Data Management Plan1. Data Collected, Formats, and StandardsThe proposed research will produce raw DNA sequence data, host plan and insectabundance data, experimental measurements, and cuticular hydrocarbon (CHC) pro-files. I will generate the DNA sequence data on an Illumina HiSeq 2500/4500 and storethe data in a series of fastq files, with one file per sequenced DNA pool (PoolSeq)or individual butterfly (GBS). These data will include sequences from ∼10,000 wild-caught Lycaeides butterflies and 2000 experimental butterfly larvae. My lab and I willprocess these raw sequence data by filtering out low-quality or non-target sequences.We will then align the remaining sequences to the Lycaeides melissa genome. We willstore the processed alignments in the standard bam format (a binary representation ofthe sam format). We will further process the sequence data by identifying variable nu-cleotides and calculating genotype likelihoods and store this processed data as a singlevcf or bcf file per project or experiment. We will store all scripts used to process thedata and relevant command line options in ‘readme’ files with the data files and onGitHub.We will generate biodiversity count data at 10 focal sites each year of the project.These data will include the UTM coordinates for each site and presence or abundancecounts of adult Lycaeides butterflies, other insects (including ants) and arachnids, andthe local host plant (Lupinus argenteus or Astragalus miser) identified at each site.We will store these data in csv formatted ASCII text files. We will also retain theoriginal data sheets and field notebooks used to record these data.Experimental data generated by the proposed research are measures of larval weightfor experimental larvae from 2000 caterpillars (Obj. 2). We will store these data in csvformatted ASCII text files with the experimental results and metadata, such as sourcepopulation, family, temperature treatment, and collection and rearing dates. We willalso retain laboratory and field notebooks with these original data.The CHC data will consist of retention time, flame ionization, and mass/charge ratiodetermined through electron ionization for compounds separated via solid phase chro-matography. These will include absorption and mass spectra for 2000-3000 caterpillars.These data, and the instrumentation and processing methods, will be stored on thecomputer associated with GC at the Nevada Institute of Chemical Ecology and onmy storage space at the University of Utah Center for High Performance Computing.Data on samples (sample ID, population ID, weight) will be stored as csv files. Wewill also retain laboratory and field notebooks with original sample data as well asdetailed steps completed in the extraction process.2. Data Storage and PreservationWe will store all primary and processed DNA sequence data on central computerservers with RAID arrays at the University of Utah Center for High PerformanceComputing (CHPC). I currently have 72 TB of storage space on these computers, andI have requested funds for additional storage to phase out older storage and buildnew capacity for the data generated by the proposed project. Data on these storage2servers are regularly and automatically backed-up. This includes two sets of quarterlytape back-ups (for all data) and weekly back-ups of active projects and data to anoff-site ceph storage device (20 TB is available). As an extra precaution, raw sequencedata will also be mirrored to USU’s google drive account. I will also deposit the rawsequence data at NCBI’s sequence read archive (SRA).All other data will also be stored on local computers in the Gompert lab and at theUniversity of Utah CHPC to guard against loss of data. We will also deposit thesedata on DRYAD for long-term storage. The DRYAD submissions will include detailsof the procedures used to generate the data and information about analyses of the dataas metadata.3. Dissemination Methods and Policies for Data SharingWe will make all sequence data and other data freely available through the open accessrepositories: NCBI’s SRA and DRYAD. These data will become available as soon asthe first associated manuscript is published and they will be made available indefinitely.Any data not published by the end of grant period (April 2024), will be made availableat that time. The metadata in these repositories will contain all of the informationneeded for other scientists to reuse these data and recreate our analyses of them.My commitment to free and open exchange in science will extend beyond data sharing.Software developed as part of this project will be made freely (i.e. open-source and nomonetary fee) available to academic and non-academic users under the GNU GeneralPublic License v2. This ensures that the programs and their source code will beavailable to all to use, modify and reuse so long as they grant the same rights toothers. Source code and binaries will be deposited on SourceForge and be availablevia my website. Manuals and examples will be provided with the software. I will alsoprioritize publishing papers from this project in open access journals or those that havean open access option (which I will take advantage of; funds have been requested forthis). Course materials from my courses will also be made freely available online for self-paced study by students anywhere in the world (USU has a long-standing commitmentto distance education and has the resources necessary to ensure the on-line course issuccessful).4. Roles and ResponsibilitiesI will take the lead and primary responsibility for coordinating computer data storageand access. I will meet regularly with the post-doc and graduate students working onthe project to discuss data management and ensure that all protocols for proper databack-up and access are being followed. While I will make all decisions about local datastorage and access, decisions regarding long-term data storage at NCBI’s SRA and onDRYAD will be made by the individuals in charge of those repositories.

CAREER: An integrated approach to understanding selection and evolution in heterogeneous environments

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CAREER: An integrated approach to understanding selection and evolution in heterogeneous environments

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