B--IN - INDIANA ES FIELD OFFICE - BAT GENOMIC ASSESSM

1 STATEMENT OF WORK Commercial Service (NAICS 541715) Genomic Assessment of the Federally Endangered Indiana Bat PR Number: 0044051176 1. General 1.1 Project Description. Who: Indiana Ecological Services Field Office (INFO) 620 South Walker Street Bloomington, IN 47403 What: Genomic Assessment of the Federally Endangered Indiana Bat Type of Services: Genomic analysis of Indiana bat, interpretation of analysis, and results report Where: Using samples collected throughout the Indiana bat’s range by various partners, the successful recipient will complete analyses at a suitable genetics and isotope laboratory(s). 1.2 Purpose/End Application: The U.S. Fish and Wildlife Service (FWS) requires a genomic analysis to better assess genetic diversity, population structure, connectivity, candidate adaptive differentiation, and potential impacts of stressors on the Indiana bat. These data will inform conservation planning and support the potential identification of biologically meaningful representation (i.e., adaptive capacity) units. Currently, we are reviewing the status of the Indiana bat, a species listed as ‘endangered’ under the Endangered Species Act of 1973 (ESA). Up-to-date information on the species’ genetic diversity, population structure, and potential adaptive differentiation is important for understanding the current and future condition of the species. As a part of this project, an updated range-wide genomic analysis will inform our evaluation of the species’ resiliency (ability to withstand to stochastic events), redundancy (ability to withstand catastrophic events), and representation (ability to adapt to environmental change), which are foundational to a species status assessment. In addition, the genomic assessment will 1) generate range-wide, baseline population genomic estimates of genetic diversity, population differentiation, and (if possible) contemporary effective population size, 2) assess the biological accuracy of established recovery units, and 3) perform foundational exploratory research of the genomic health of this species aimed at improving our understanding of impacts from white-nose syndrome. -- 1 of 7 -- 2 1.3 Contractor Qualifications: The contractor shall demonstrate: • Documented experience preparing, extracting and sequencing DNA from small biological samples and conducting genomic analyses utilizing the RADseq technique or similar approaches. • Ability to report, archive, and document analytical procedures, code, and workflows consistent with scientific best practices. 1.4 Other: The statutory authority for this work is provided under the Endangered Species Act of 1973 (ESA), which establishes protections for fish, wildlife, and plants that are classified as threatened and endangered species. The ESA requires preparation and implementation of plans for the recovery of each listed species. This research specifically supports Recovery Action 3.5.3 Conduct additional studies of Indiana bat population genetics based on sampling at hibernacula from the 2007 Draft Indiana Bat Recovery Plan. 2. Place of Performance and Period of Performance Place of Performance: Suitable genetics lab with qualified wildlife geneticists Period of Performance: October 2026 – December 2027 2.1 Place of Performance Work is to be performed at the contractor site. 2.2 Period of Performance Performance Start Date: October 1, 2026 Performance End Date: December 31, 2027 Over the past two years, INFO, in coordination with partners, has actively collected genetic samples (i.e., wing punches) throughout the range of the Indiana bat. The successful recipient would begin processing and analyzing available samples in early October 2026. A limited number of additional samples may continue to be collected by FWS biologists and partners at targeted hibernacula through March 2027. 2.3 Normal duty hours are Monday through Friday 8:00 a.m. - 4:30 p.m. In the event of emergencies, Contractor shall provide contact information. 2.4 Non-duty hours include week nights, weekends, and Government holidays (New Year’s Day, Martin Luther King Jr.s’s Birthday, Washington’s Birthday, Memorial Day, Juneteenth, Independence Day, Labor Day, Columbus Day, Veterans Day, Thanksgiving Day, Christmas Day). -- 2 of 7 -- 3 3. Scope 3.1 The contractor shall extract total genomic DNA from all samples provided by the FWS and cooperating partners, generate sequence reads via restriction site-associated sequencing (RADseq) library prep, sequencing via the Illumina NovaSeq X+ platform, conduct bioinformatic processing, analyze the resultant data, and submit a report utilizing their expertise, services and training. Task 1: DNA Extraction and Quality Control • Extract high-quality total genomic DNA from approximately 200-400 tissue or DNA samples (e.g., wing punches from 20 individual bats collected from approximately 10 different sites across the range). • Perform DNA quantification and quality assessments to ensure suitability for sequencing. Task 2: RADseq Library Preparation and Sequencing • Prepare RADseq libraries using a protocol appropriate for the target taxa. • Sequence libraries on the Illumina NovaSeq X Plus platform or equivalent, generating sufficient depth for individual-level inference (i.e., >15-20x coverage per individual). Task 3: Bioinformatic Processing • Process raw sequencing reads, including demultiplexing, adapter removal, and quality filtering. • Perform de novo or reference-guided alignment and SNP discovery. • Filter SNPs based on quality metrics and prepare datasets suitable for downstream analyses. Task 4: Genomic Analysis • Conduct PCA and STRUCTURE/Admixture (or similar population assignment analysis) to identify potential distinct genetic clusters. • Estimate gene flow and connectivity among populations using appropriate statistical models • Estimate genetic diversity metrics and contemporary effective population sizes of populations. • Evaluate genetic signatures of stress or re…