12G0, 4120, FY27 Roundtail Chub Genomics

Notice of Proposed Sole Source Scope of Work and Sole Source Justification NPSS1 PMAA 2026*0210 FY27 Roundtail Chub Genomics in Colorado Scope of Services See attached Scope of Work. Schedule and Term of Award A Contract will be executed as soon as practical. The Sole Source Procurement end date is 6/30/2027. Budget Colorado Parks and Wildlife (CPW) has budgeted an approximate amount of $120,750.00 for the purchase. Sole Source Justification CPW wants to purchase these services from Brigham Young University (BYU) genetics lab, specifically Dr. Evans, because the state of Utah is doing a very similar project with Roundtail Chub and Dr. Evans is providing whole genome sequencing and genetic analysis services. Having the sequencing and genetics conducted in the same lab by the same individual allows CPW to easily and effectively compare results; this is necessary because our Roundtail Chub populations in Colorado are connected to the Utah Roundtail populations. Roundtail Chub can swim large distances. In addition, if a different lab provided these services there would be added lab and batch effects making comparison of Colorado's results and Utah's results more difficult and time consuming to analyze, which would be detrimental to the projects’ timeline goals. Contact and Submittal Submit any questions or any submittal item via email with the solicitation number NPSS1 PMAA 2026*0210 in the subject line to: Jeanette Stroud Department of Natural Resources, Purchasing Office Jeanette.Stroud@state.co.us 1 Submittal Items This Notice of Proposed Sole Source (NPSS1) has been posted to invite vendors who may be able to offer the services noted in the Scope of Work to respond and confirm their capabilities. If it is determined that more than one vendor can provide the services needed, the purchase will be formally solicited. In order to demonstrate your ability to fulfill the need, please send an email with a brief one-page cover letter (as an attachment), signed by the sole proprietor , individual or someone authorized to bind your firm which includes: Vendor Name, Vendor Address, including City, State, and zip code, phone number , and email address. In your letter describe how your firm, considering the ability of Brigham Young University and the services they are offering, could supply this service. Important: Please be aware that this is not a solicitation for a proposal, quotation, or pricing. This is simply a notification that the Department of Natural Resources Purchasing Office intends to issue a sole source contract award as outlined above. This is an opportunity for other entities to challenge the sole source status of the contract award. If a challenge is received, unless proved to be unfounded, a solicitation will be issued. Entities that are not prepared to go forward and respond to a solicitation for this work are not encouraged to submit a challenge. 2 Scope of Work Roundtail Chub Genomics in Colorado Project Description : Roundtail Chub (RTC, Gila robusta ) are endemic to the Colorado River Basin and have been extirpated from 45 percent of their historical range (Bezzerides and Bestgen 2002). Severe range contraction in the lower Colorado River Basin (below Glen Canyon Dam) led to a federal petition to list lower Colorado Basin RTC as a distinct population segment, initiating a Species Status Assessment review . The Species Status Assessment review resulted with a “not warranted” finding but underscored the significant decline and worrisome trend for RTC in both the lower and upper Colorado River Basin. During the recent Colorado State Wildlife Action Plan (SWAP) revision (2025), species experts determined that RTC are “extremely vulnerable” under all three criteria (abundance, distribution, and trend), the most severe status among the “three species” (i.e., Bluehead Sucker , Flannelmouth Sucker , Roundtail Chub). The Range Wide Conservation Agreement and Strategy , of which Colorado Parks and Wildlife (CPW) is a signatory , mandates conservation actions to “genetically and morphologically characterize populations” for the “three species”. Prior research conducted in the lower CO basin (e.g., Arizona) determined that RTC varies considerably genetically when separated geographically (Suchocki et al 2023). Similar conclusions were found in an analysis of closely related Rio Grande Chub ( Gila pandora ), a Colorado State Species of Concern (Mussmann and York 2018). These results highlight the need to investigate Colorado’ s RTC populations across all river drainages and in the hatchery . CPW currently maintains four broodstocks of RTC at the Native Aquatic Species Restoration Facility (NASRF), all originating from the San Juan Basin (Mancos R., La Plata R., San Juan R., and Navajo R.) The original impetus for maintaining these specific broodstocks is twofold: First, severe droughts in the early 2000’ s caused excessive stream drying in the SW Region and a legitimate concern that populations (and potentially unique genetic lineages) could be extirpated. This led to timely fish salvage efforts coordinated between CPW and tribal biologists to bring RTC to NASRF . Secondly , tribal partners (Jicarilla-Apache and Southern Ute Nations) have placed a great conservation emphasis on RTC in the Upper San Juan Basin (above Navajo Reservoir) and have partnered with CPW to manage brood and stock fish to maintain populations. The upper San Juan population of RTC is of particular conservation value, as RTC are virtually extirpated in the mainstem San Juan River below Navajo Reservoir—an unfortunate circumstance that can be attributed, in part, to the 1962 intentional poisoning of over 100 Km of river to remove “rough fish” and subsequent inundation of prime habitat to create Navajo Reservoir . Roundtail Chub were considered one of the most common species killed in this effort (Olson 1962). While priority has been placed on SW Region brood sources to date, alarming declines in other major basins (e.g., Dolores and Yampa) underscores the need to evaluate RTC genetic diversity across Colorado to prioritize our management actions. Colorado Parks and Wildlife plans to determine the genetic population structure and management units (Mus) of Colorado RTC populations, an effort that mirrors a similar project undertaken in Utah that defined genetic management units of Utah’ s nine RTC populations. This project’ s results will be used to maximize the potential of NASRF's propagation program and provide managers with important and updated genetic structure and distribution information for RTC across inhabited river drainages in Colorado. Expected results should determine the population structure, genetic variation, determine management units (MUs), quantify connectivity among populations (F st ), effective population sizes, and genetic diver gence among populations. Managers can then determine necessary steps to bring additional genetic diversity from the wild into NASRF , or conversely , combine existing brood sources that are genetically similar to maximize existing genetic diversity and streamline operations at NASRF . Additionally , wild population genetics information can be used to better understand RTC populations across Colorado. This study will involve collaboration and data collection with CPW’ s Native Species Coordinator , CPW Aquatic Research Scientists, and other members of CPW’ s Native Aquatic Species Team. Genetic samples (fin clips) will be collected from each of the major river drainages containing RTC populations in Colorado, as well as from historical samples. Roundtail Chub populations include the: Yampa River , White River , Colorado River , Gunnison River , Dolores River , Upper San Juan River (above Navajo Reservoir), Lower San Juan River (below Navajo Reservoir). Samples will be collected as part of routine statewide monitoring efforts and with targeted sampling. During these efforts, fin clips will be taken from 30 RTC from each population as feasible. Sampling efforts will span two fiscal years (FY 25-26, FY26-27). Unfortunately , hybridization has been documented and studied in Lower San Juan Basin tributaries following an accidental introduction of RCH, necessitating the development of an appropriate genetic technique to more definitively identify these hybrids (Bestgen et al. 2021). Wild Rio Grande Chub (RCH) and Humpback Chub (HBC) populations will also be sampled due to species overlap to enhance our ability to monitor chub hybridization (30 fin clips per population). Samples from each fish will be individually stored in 2 ml vials and preserved in 95% ethanol. Samples will be sent to Dr. R. Paul Evans (BYU) for DNA extraction and sequencing. Having DNA extraction, library prep and genotyping done by Dr. R Paul Evans reduces the batch effects and allows for better comparison of genetic data to Utah’ s samples. Results will be used to establish the genetic status of RTC in Colorado and will be compared to data collected from Utah’ s populations. This research is expected to result in an understanding of Colorado’ s Roundtail Chub population structure, genetic variation, determine management units (MUs), quantify connectivity among populations, effective population sizes, and genetic diver gence among populations. Schedule: Task April - June 26 July - Sept. 26 Oct 26- Dec 26 Jan 2027– March 2027 April 27 – June 27 Sample Collection x x x x Genomic lab work & sequencing x x x Genomic analyses x x x Progress Report x x x CPW Final Report x Deliverables: This research is expected to result in an understanding of Colorado’ s Roundtail Chub population structure, genetic variation, determine management units (MUs), quantify connectivity among populations, effective population sizes, and genetic diver gence among populations. Professional Communication : A CPW staff member must be a coauthor of completed and submitted manuscript(s) based on Colorado’ s Roundtail Chub genomics data, if results are deemed appropriate. Progress Report(s): Quarterly progress reports indicating work that has been done (number of samples processed, etc). Progress reports are due: July 1 st , Oct 1 st , Jan 1 st , and April 1 st of each quarter outlined in the schedule. Final Report : BYU shall submit a final report no later than June 30 th , 2028. Final report should include brief introduction, molecular methods (what, how and why) used, methods for data and statistical analysis, results and discussion. Data : An organized and well documented copy of all data and computational code, which may include but is not limited to: lab process sheets, raw sequencing data (.fastq files), data processing scripts (bash scripts and R scripts), bioinformatic scripts, Snakemake files, data processing environment details, R environment and project files, and population genetics code and procedures; will be provided on a single hard drive or multiple hard drives to Colorado Parks and Wildlife at the completion of the project. R eferences: Bestgen, K.R., M.R. Haworth, and A.J. Hink. 2021. Identification of hybrids between native and nonnative Gila in the San Juan River drainage, Colorado, aids removal management. Fort Collins: Draft Report, Colorado State University , Larval Fish Laboratory Contribution 224. Bezzerides, N., and K. R. Bestgen. 2002. Status review of Roundtail Chub Gila robusta, Flannelmouth Sucker Catostomus latipinnis, and Bluehead Sucker Catostomus discobolus in the Colorado River basin. Fort Collins: Final Report, Colorado State University , Larval Fish Laboratory Contribution 118. Mussmann S.M and G. York. 2018. Genetic evaluation of Rio Grande chub (Gila pandora) broodstock from southern Colorado. U.S. Fish and Wildlife Service Region 2. Albuquerque, NM. Olson, H. F. 1962. Rehabilitation of the San Juan River . Job Completion Report, Federal Aid Project F-19-D-4. Santa Fe: New Mexico Department of Game and Fish. Suchocki, C.R., Ka‘apu-L yons, C., Copus, J.M. et al. Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae). Sci Rep 13, 15810 (2023). https://doi.or g/10.1038/s41598-023-41719-9