YOTO Study_Single Source Justification FAR 13 Under SAT.pdf

Single Source/Brand Name Justification United States Department of Agriculture

FAR 13.106-1(b)(1) – Simplified Acquisitions

1. Identification of the agency and the contracting office.

US Forest Service, Eldorado National Forest.

2. Description of supply or service required to meet the agency’s needs.

This contract is part of a larger research effort designed to investigate the genetic nature of a Federally listed threatened species, the Yosemite toad (Anaxyrus canorus) on the Eldorado National Forest. The work to be performed under this contract consists of technical assistance with the genetics lab and analysis of the data produced. Specific duties under the contract will include:

1. Work with the genetics lab to address any technical issues and ensure lab protocols are compatible with those of Dr. Paul Maier as detailed in Maier et al., 2019.

2. Provide banked Yosemite toad tissues to the genetics lab as needed to validate suitability of lab protocols.

3. Perform all bioinformatics and data processing including:

a. Analyzing data from pilot studies to determine suitability of lab protocols and ensure data compatibility with Dr. Maier’s existing Yosemite toad ddRADseq library.

b. Processing of raw genetic sequencing data for Western toad and suspected hybrids following the general procedures of Maier et al., (2019).

c. Assess ddRADseq libraries for basic genetic statistics and any issues that may impact the effectiveness of marker selection (i.e., closely related individuals, missing genotypes, low diversity, paralogues, etc.).

d. Generate a de novo or reference guided assembly, identify alleles, identify homologues, and call Single Nucleotide Polymorphisms (SNPs).

i. Write scripts to encode sequence data into any necessary genotype formats, including RAD haplotype format.

e. Use maximum likelihood and Bayesian approaches to compare Western toad and Yosemite toad ddRADseq libraries, and develop a panel for assessing hybridization (i.e., generations since admixture and species symmetry).

i. Test the accuracy and precision of the hybrid panel on genetic data from known or suspected hybrids or using a simulation approach.

ii. Classify hybrid status for unknown samples using the reference ddRADseq library and the identified markers.

f. A final report detailing processes, procedures, and results found.

Deliverables for this contract will be due by the end of the Grant period which ends on 12/31/2024. However, there is a possibility to extend the Grant period for a year if needed. If an extension occurs, the deliverable date will be extended for one year (12/31/2025)

3. The rationale or circumstances for limiting competition.

The goal of this research project is to develop a genetic assay capable of identifying inter-species hybridization between the threatened Yosemite toad and the common Western toad (Anaxyrus boreus).

We have decided to use a genetic approach know as “double digest Restriction Site Associated DNA sequencing” (ddRADseq) because (1) it offeres the best chance for identifying markers capable of revealing hybridization in these two closely related species and (2) a RADseq library for the Yosemite toad is already available (Maier 2019). Using existing data (i.e., Dr. Maier’s ddRADseq library) will eliminate the need to independently develop data for the Yosemite toad.

The project will be based entirely on previous work on the Yosemite toad by Dr. Paul Maier (Maier et al., 2019). Dr. Maier developed a genetic library for the Yosemite toad using the ddRADseq technique.

We plan to use Dr. Maier’s Yosemite toad library and develop a compatable library for the Western toad using the same technique. The two libraries will then be compared to identify suitable markers for the development of a hybrid assay. Since we plan to compare the new libray to the existing library, ddRADseq compatability between the two libraries is essentiual for the project to work. Post-processing of the raw genetic data must also follow the original approach taken with the existing Yosemite toad library. Therefore, it is necessary that the services described above be performed by Dr. Maier to:

1. Ensure lab protocols are compatable with the protocols used to develop the Yosemite toad genetic library. This is essential because there is no standard ddRADseq approach and labs vary widely on how they implement the technique. A full technical description is beyond the scope of this document, but, in simple terms, adherance to the fundamental elements of Dr. Maier’s protocol is necessary to ensure we are comparing the same regions of the genome between species. If this is not acheieved the project will not work and Dr. Maier is the only person that can ensure adherance to the details that will be necessary for success.

2. The processing of the raw genetic data produced by the lab and the development of ddRADseq libraries for Western toad and suspected hybrids will need to follow the general procedures of Maier (2019). Again this is necessary for compatabilty between libraries and Dr. Maier’s previous work. Dr. Maier wrote his own Python scripts for some of this work and that needs to be replicated with the new data. Dr. Maier is the only person that can ensure this process is replicated accurately.

3. Dr. Maier has banked Yosemite toad tissue, used in the previous work, that we need to use to verify laboratory ddRADseq protocols are isolating the same regions of the genome as the previous work.

The services we require are directly related to and dependent upon previous work done by Dr. Paul Maier. Furthermore, the use of Dr. Maier’s previous research provides a solid basis to start from and will save the US Government a substantial amount of money that would otherwise be needed if we started from scratch (i.e., if we also needed to develop the Yosemite toad library). Independently developing data on the Yosemite toad would require many hours of field work, travel, office work, and laboratory costs and would likely double the cost of the entire project.

4. A description of the market research conducted and the results or a statement of the reason market research was not conducted.

Market research for this contract consisted of online research to document the average salary for a PhD level geneticist. No effort was made to identify other potential service providers because there is no other provider that can meet the requirements of this contract (i.e., no other person that knows the details of Dr. Maier’s previous project).

The cost for Dr. Maier’s services equal an annual salary of aproximately $110,000. The Bureu of Labor Statistics (BLS) salary data does not contain a category for genticists, but the proposed level of pay is comparable to the BLS average pay for a Biochemist (19-1021; $128,440) and a generic Biological Scientist (19-1020; $98,260) involved in Research and Development in the Physical, Engineering, and Life Sciences (NAICS 541600; Attachement 1). It should be noted that the BLS does not break down salary by education level so a PhD level geneticist should be on the high end of this scale. This pay level is also compatable with estimates of the average salary for a research geneticist in the state of California (Attachment 2). However, this proposed pay scale is considerably less than the median salary for an early career PhD level geneticist without a medical degree ($115,450) according to a survey by the American College of Medical Genetics and Genomics (Attachment 3).

5. Estimated price, including all options, if applicable.

The estimated cost for Dr Maier’s service is detailed in the table below:

Rate $ 53.00 UOM hour Quantity 320 Total $ $16920 Grant Request $ $16,920

The time required to complete this task is an estimate based on discussions with Dr. Maier. However, genetic analyses are very complex endeavors and there is the potential that more time may be needed.

While $16,920 was budgeted for this task, there is some room in the budget for cost overruns should more time be needed.

6. Recommended source(s).

Dr. Paul Maier paulm@genebygene.com

References

Maier, P. A., A. G. Vandergast, S. M. Ostoja, A. Aguilar, and A.J. Bohonak. 2019. Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus). Evolution, Vol. 73, pp. 2476–2496.

mailto:paulm@genebygene.com

Certifications

Supporting data that is the responsibility of technical or requirements personnel and which form the basis for this justification are accurate and complete to the best of my knowledge.

Jeffrey Mabe PhD, Aquatic Biologist, Eldorado National Forest Insert Name of Program or Technical Personnel Insert Title of Program/Technical Personnel

The information contained in this justification is accurate and complete to the best of my knowledge and belief and in accordance with Federal Acquisition Regulation 13.106-1(b)(1), I hereby determine the circumstances described above deem only one source, or limited sources, reasonably available and competition is precluded for the reasons indicated in this document.

Robert Briney Contracting Officer