I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?

To determine the number of paternal parents in amphibian offspring using molecular markers such as STRs or SNPs, one can analyze the genetic variation within the egg clutches. By examining highly polymorphic markers, you can compare the alleles present in the offspring. The presence of multiple, unique paternal alleles at each marker locus indicates multiple paternal contributors. High marker polymorphism is crucial for accurate inference, and methods like Bayesian analyses (e.g., COLONY) can be effective despite some biases [1][2][3]. SNPs and STRs both perform well, although SNPs can sometimes offer better resolution in complex scenarios [4][5][6].

Reference

[1] Weinman, L. R., Solomon, J., & Rubenstein, D. (2015). A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird. Molecular Ecology Resources, 15.

[2] Villanueva, B., Verspoor, E., & Visscher, P. (2002). Parental assignment in fish using microsatellite genetic markers with finite numbers of parents and offspring.. Animal genetics, 33 1, 33-41 .

[3] Liu, X., Zhao, G., Wang, Z., Cai, M., Ye, H., & Wang, Q. (2012). Parentage assignment and parental contribution analysis in large yellow croaker Larimichthys crocea using microsatellite markers. Current Zoology, 58, 244-249.

[4] Flanagan, S., & Jones, A. (2019). The future of parentage analysis: From microsatellites to SNPs and beyond. Molecular Ecology, 28, 544 - 567.

[5] Rodríguez-Barreto, D., Consuegra, S., Consuegra, S., Jérez, S., Cejas, J., Martín, V., & Lorenzo, A. (2013). Using molecular markers for pedigree reconstruction of the greater amberjack (Seriola dumerili) in the absence of parental information.. Animal genetics, 44 5, 596-600 .

[6] Cockburn, A., Peñalba, J. V., Jaccoud, D., Kilian, A., Brouwer, L., Double, M., Margraf, N., Osmond, H. L., Kruuk, L., & Pol, M. v. d. (2021). hiphop: Improved paternity assignment among close relatives using a simple exclusion method for biallelic markers. Molecular Ecology Resources, 21.

Yes, this is a very solvable investigation.

Step 1: read what is already known. There is no substitute for doing your own deep dive into the literature.

Step 2: Talk with your mentor! They can assist you in outlining a plan.

Step 3: Decide how you will analyze your data BEFORE you collect any data. Trust me on this one.

Step 4: Start small. Test out one or two markers with a good set of controls. Don't scale up until you are certain that your assay is working.

This is going to take a big chunk of your time. As my research mentor said "You can't rush quality". And there are no shortcuts. You are going to have to create your own research plan.

Good luck!