DOI: 10.5061/dryad.n02v6wwt2
title: Conservation genomics of Wyethia reticulata (Asteraceae)

description: 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.
description: 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
 <i>genet_dist</i> function of the R package
 <i>RClone</i> 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
 (<i>F<sub>st</sub></i>) among all
 locales. Calculated
 using the R package <i>adegenet</i>, 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.