Abstract
The original PumaPlex is a high-throughput assay developed to genotype 25 single nucleotide polymorphisms (SNPs) in pumas (Puma concolor). Here, we describe the development of PumaPlex100 – an expanded version of the original assay that now genotypes > 100 SNPs. We tested 142 candidate SNPs and developed a panel of 101 polymorphic loci, which are spread across four multiplexes and suitable for genotyping of non-invasive samples. This panel will provide researchers a set of standardized markers, that can be analyzed with minimal bioinformatic skills, for the assessment of population structure and genetic diversity. These SNPs will serve as an important resource for the continued genetic monitoring of this species, especially monitoring through non-invasive sampling.
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References
Carroll EL, Bruford MW, DeWoody JA et al (2018) Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 11:1094–1119. https://doi.org/10.1111/eva.12600
Cassaigne I, Medellin RA, Thompson RW et al (2016) Diet of pumas (Puma concolor) in Sonora, Mexico as determined by GPS kill sites and molecular identified scat, with comments on jaguar (Panthera onca) diet. Southwestern Naturalist 61:125–132. https://doi.org/10.1894/0038-4909-61.2.125
Cougar Management Guidelines Working Group (2005) Cougar management guidelines, 1st edn. WildFutures, Bainbridge Island, WA
Eriksson CE, Ruprecht J, Levi T (2020) More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing. Mol Ecol Resour 20:1505–1516. https://doi.org/10.1111/1755-0998.13208
Fernández ME, Goszczynski DE, Lirón JP et al (2013) Comparison of the effectiveness of microsatellites and SNP panels for genetic identificaiton, traceability and assessment of parentage in an inbred Angus herd. Genet Mol Biol 36:185–191. https://doi.org/10.1080/00380768.1996.10416639
Fitak RR, Naidu A, Thompson RW, Culver M (2016) A new panel of SNP markers for the individual identification of North American Pumas. J Fish Wildlife Manag 7:13–27. https://doi.org/10.3996/112014-JFWM-080
Gärke C, Ytournel F, Bed’Hom B et al (2012) Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations. Anim Genet 43:419–428. https://doi.org/10.1111/j.1365-2052.2011.02284.x
Gabriel S, Ziaugra L, Tabbaa, D (2009) SNP genotyping using the Sequenom MassARRAY iPLEX platform. Current protocols in human genetics, Chapter 2, Unit 2.12. https://doi.org/https://doi.org/10.1002/0471142905.hg0212s60
Goossens B, Sharma R, Othman N et al (2016) Habitat fragmentation and genetic diversity in natural populations of the Bornean elephant: implications for conservation. Biol Cons 196:80–92. https://doi.org/10.1016/j.biocon.2016.02.008
Henriques D, Browne KA, Barnett MW et al (2018) High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool. Sci Rep 8:345. https://doi.org/10.1038/s41598-018-26932-1
McKinney TD (2011) Cougar research and management needs. In: Jenks JA (ed) Managing Cougars in North America. Berryman Institute Press, Logan, UT, pp 189–200
Morin PA, Archer FI, Pease VL et al (2012) Empirical comparison of single nucleotide polymorphisms and microsatellites for population and demographic analyses of bowhead whales. Endangered Species Res 19:129–147. https://doi.org/10.3354/esr00459
Natesh M, Taylor RW, Truelove NK et al (2019) Empowering conservation practice with efficient and economical genotyping from poor quality samples. Methods Ecol Evolut 2019:1–7. https://doi.org/10.1111/2041-210X.13173
Ochoa A, Onorato DP, Fitak RR et al (2019) De novo assembly and annotation from parental and F1 Puma genomes of the Florida Panther genetic Restoration Program. G3 Genes Genomes Genet 9:3531–3536. https://doi.org/10.1534/g3.119.400629
Ochoa A, Onorato DP, Fitak RR et al (2017) Evolutionary and functional mitogenomics associated with the genetic restoration of the Florida panther. J Hered 108:449–455. https://doi.org/10.1093/jhered/esx015
O’Leary SJ, Puritz JB, Willis SC et al (2018) These aren’t the loci you’re looking for: principles of effective SNP filtering for molecular ecologists. Mol Ecol 27:3193–3206. https://doi.org/10.1111/mec.14792
Saremi NF, Supple MA, Byrne A et al (2019) Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nat Commun. https://doi.org/10.1038/s41467-019-12741-1
Trumbo DR, Salerno PE, Logan KA et al (2019) Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide. Mol Ecol 28:4926–4940. https://doi.org/10.1111/mec.15261
von Thaden A, Nowak C, Tiesmeyer A et al (2020) Applying genomic data in wildlife monitoring: development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.13136
Whittaker D (2011) Managing Cougars in North America. In: Jenks JA (ed) Managing Cougars in North America. Berryman Institute Press, Logan, UT, pp 9–13
Acknowledgements
We would like to thank those who provided samples or extracted DNA, specifically Ron Thompson, Ashwin Naidu, Ivonne Cassaigne, Karla Vargas, and Alex Ochoa. We thank the University of Arizona Graduate and Professional Student Council (GPSC) for funding through a Research and Project (ReaP) Grant. We are deeply indebted to Colleen Ramsower and Crystal Richt at the University of Arizona Genetics Core for assistance with Sequenom genotyping. We are grateful to Alex Ochoa for comments on earlier drafts of this manuscript. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
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Erwin, J.A., Fitak, R.R. & Culver, M. PumaPlex100: an expanded tool for puma SNP genotyping with low-yield DNA. Conservation Genet Resour 13, 341–343 (2021). https://doi.org/10.1007/s12686-021-01206-7
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DOI: https://doi.org/10.1007/s12686-021-01206-7