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Updated: May 15, 2025
A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes
Published on: March 1, 2022
Precise lineage tracking using molecular barcodes demonstrates fitness trade-offs for ivermectin resistance in
Zachary C Stevenson1, Eleanor Laufer1, Annette O Estevez1
1Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97401, United States.
Abstract:
A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci vary with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans to implement the first randomly inserted genomic-barcode fitness experiment within an animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, with the frequency of each barcode then being measured at multiple time points via sequencing at deep coverage and used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wild-type genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2 nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high-precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.
