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Conservation genomics of Wyethia reticulata (Asteraceae)

Citation

Burge, Dylan (2020), Conservation genomics of Wyethia reticulata (Asteraceae), Dryad, Dataset, https://doi.org/10.5061/dryad.n02v6wwt2

Abstract

Wyethia reticulata is a rare perennial herb found only on gabbro-derived soils of the Pine Hill formation in the Sierra Nevada foothills of El Dorado County, California. Wyethia reticulata is capable of both vegetative (clonal) and sexual reproduction, although the former is thought to be more common than the latter, with sexual reproduction tied to fire. The potential dominance of vegetative reproduction has conservation implications for W. reticulata, as populations could appear healthy in terms of stand density, while losing genetic diversity due to a lack of sexual recruitment. Past genetic assessments of W. reticulata relied on low-resolution markers from a small number of populations and did not directly address conservation issues. Here, double-digest random amplified DNA sequencing was used to develop a high-resolution genomic dataset for a sample of 168 W. reticulata samples from seven locations that represent every known population center of the species. The data was used to 1) calculate the frequency of asexual reproduction, 2) determine which populations contain unique genetic variation, and 3) test whether there are any ecological correlates of genetic patterns. In contrast to past genetic research, the results presented here indicate that clonality is not common; less than 2% of plants were identified as being derived from asexual reproduction. Nevertheless, some locations seem to be more affected by asexuality than others; the index of association varied from 4.4 to 19.4 (average = 10.9). Genetic differentiation among locations was low (Fst 0.03-0.04). However, clustering identified three distinct population segments that were not previously recognized. Elevation was the only environmental variable significantly associated with genetic differentiation. Based on these results, it is recommended that conservation effort be focused on genetically isolated population segments.

Usage Notes

Appendix S1. Data on sampled plants, including locale names, GPS coordinates, climatic and soil data, sequencing coverage, and NCBI accession numbers. Duplicate samples (biological replicates) are indicated with the letter ‘D’ at the end of the sample name. For definition of the terms AET, CWD, PPT, TMIN, and TMAX, see the Materials and Methods section.

Appendix S2. Frequency distributions of allele distances for each locale. From the genet_dist function of the R package RClone v. 1.0.2 (Bailleul et al. 2016).

Appendix S3. VCF file for raw genotypes. Raw genotypic data resulting from the allele calling carried out by Floragenex.

Appendix S4. VCF file for filtered genotypes. Filtered genotypic data resulting from filtering of discordant loci (those that varied between biological replicates).

Appendix S5. Genetic differentiation (Fst) among all locales. Calculated using the R package adegenet, v. 1.3-1 (Jombart and Ahmed 2011).

Appendix S6. Results of Evanno method for assessing optimal K. Based on output from STRUCTURE HARVESTER (Earl and vonHoldt 2012).

Appendix S7. Biplot for results of redundancy analyses (RDA) on climate, controlling for geography (latitude and longitude). The position of the sampled plants indicates their genetic relationships with one another; direction and magnitude of the vectors shows how the three analyzed factors are associated with the groupings of plants.

References Cited

Bailleul, D. S. Stoeckel, and S. Arnaud-Haond. 2016. RClone: a package to identify Multilocus Clonal Lineages and handle clonal datasets in R. Methods in Ecology and Evolution 7.

Earl, D. A., and B. M. vonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.

Jombart, T. 2008. Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403–1405.

Funding

U.S. Bureau of Land Management, Award: L16PX01835