Dataset: Sample data for Lottia genomic samples

This dataset has not been validatedPreliminary and in progressVersion 1 (2025-04-10)Dataset Type:Other Field Results

Principal Investigator: Rachael Bay (University of California-Davis)

Co-Principal Investigator: Richard K. Grosberg (University of California-Davis)

Co-Principal Investigator: Eric Sanford (University of California-Davis)

Scientist: Brenda Cameron (University of California-Davis)

Scientist: Philip Fenberg (University of Southampton)

Scientist: Erica Nielsen (University of California-Davis)

Scientist: Jacqueline Sones (University of California-Davis)

Student: Sam Walkes (University of California-Davis)


Project: Evolutionary and ecological dynamics of a contemporary climate-driven range expansion (LottiaRangeExp)


Abstract

As climatic variation re-shapes global biodiversity, understanding eco-evolutionary feedbacks during species range shifts is of increasing importance. Theory on range expansions distinguishes between two different forms: “pulled” and “pushed” waves. Pulled waves occur when the source of the expansion comes from low-density peripheral populations, while pushed waves occur when recruitment to the expanding edge is supplied by high-density populations closer to the species' core. How extreme events...

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We sampled 19 sites on the Pacific coast of North America, spanning most of the contemporary range of L. gigantea. We non-lethally excised a small piece of foot muscle tissue. For all locations except the four northern sites, we collected tissue from roughly 30 individuals per site, comprised of 10 individuals within each of the following size ranges: 10–25 mm (small), 30–40 mm (medium), and >40 mm (large). Sampling of the four northern sites (i.e., expanded range) also consisted of roughly 10 small, medium, and large individuals per site. However, as individual limpets at these four sites have been closely monitored over the past 8 years, these sites had known cohorts based on the estimated year of settlement. Size classes at sites for which we do not have monitoring data were chosen based on our data and previous growth curves (Kido & Murray, 2003) to approximately group individuals into those that settled during the MHWs, soon after the MHWs (late 2016 or late 2017), or well after the MHWs (late 2018 or late 2019). Tissue was stored in 90% ethanol at −20°C. We used the Qiagen DNAeasy extraction kit to perform DNA extractions following the manufacturer's protocols. DNA quantity and quality were assessed with Nanodrop, Qubit, and gel electrophoresis. Library preparation followed the Nextera Lite protocol, with adaptations following Rowan et al. (2019). Briefly, this consisted of normalizing samples, tagmentation, PCR, pooling samples, and bead size selection. The purified samples were run on a High Sensitivity DNA Bioanalyzer chip and then sent to BGI Genomics for whole-genome sequencing on the DNBSEQ-T7 PE150 platform on four lanes of sequencing.


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Results

Nielsen, E. S., Walkes, S., Sones, J. L., Fenberg, P. B., Paz‐García, D. A., Cameron, B. B., Grosberg, R. K., Sanford, E., & Bay, R. A. (2024). Pushed waves, trailing edges, and extreme events: Eco‐evolutionary dynamics of a geographic range shift in the owl limpet, Lottia gigantea. Global Change Biology, 30(7). Portico. https://doi.org/10.1111/gcb.17414
Methods

Kido, J., & Murray, S. (2003). Variation in owl limpetLottia giganteapopulation structures, growth rates, and gonadal production on southern California rocky shores. Marine Ecology Progress Series, 257, 111–124. https://doi.org/10.3354/meps257111
Methods

Rowan, B. A., Heavens, D., Feuerborn, T. R., Tock, A. J., Henderson, I. R., & Weigel, D. (2019). An Ultra High-DensityArabidopsis thalianaCrossover Map That Refines the Influences of Structural Variation and Epigenetic Features. Genetics, 213(3), 771–787. https://doi.org/10.1534/genetics.119.302406