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Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions

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Abstract

The field of conservation genetics is in the midst of transitioning from microsatellites to single nucleotide polymorphisms (SNPs) as part of a broader transition from genetic to genomic studies. Genomics offers the potential for more accurate estimation of individual and population parameters but at higher project costs. I calculated cost curves for multi-locus genotypes to describe how total project and per sample costs varied between microsatellite and SNP genotyping. Cost curves were calculated varying multiple parameters which influenced costs, including: number of microsatellite loci, primer multiplexing, number of samples pooled per library, sequencing costs, and variation in laborer salaries. Sequencing costs had the greatest effect on total project costs for both markers, suggesting a way to achieve the greatest savings. For microsatellites, increasing loci number had a small effect on increasing costs, although using an increasing number of multiplex panels had a significant effect. For SNPs, increasing the number of samples pooled per genotyping library resulted in the greatest cost savings; however, this was tempered somewhat by species genome size and study design parameters which could decrease per locus sequencing depth below thresholds needed for robust SNP calling. Thus, this study highlights multiple parameters to consider when designing conservation genotyping studies to maximize information while minimizing costs. I also surveyed studies that compared microsatellites and SNPs. SNPs had greater accuracy than microsatellites when SNP loci were 3–2800 fold greater. Cost curves are provided as changing parameter assumptions effects estimates.

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Acknowledgements

Sheena Feist, Jane Park, and three anonymous reviewers provided constructive feedback which improved the manuscript.

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  1. Department of Biological Sciences and the Louis Calder Center-Biological Field Station, Fordham University, 31 Whippoorwill Road, Armonk, NY, 10504, USA

    Emily E. Puckett

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Puckett, E.E. Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions. Conservation Genet Resour 9, 289–304 (2017). https://doi.org/10.1007/s12686-016-0643-7

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